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        Module&nbsp;Melding
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<h1 class="epydoc">Source Code for <a href="trunk.BIP.Bayes.Melding-module.html">Module trunk.BIP.Bayes.Melding</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">   1</tt>  <tt class="py-line"><tt class="py-comment"># -*- coding:utf-8 -*-</tt> </tt>
<a name="L2"></a><tt class="py-lineno">   2</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L3"></a><tt class="py-lineno">   3</tt>  <tt class="py-line"><tt class="py-comment"># Name:        Melding.py</tt> </tt>
<a name="L4"></a><tt class="py-lineno">   4</tt>  <tt class="py-line"><tt class="py-comment"># Purpose:     The Bayesian melding Class provides</tt> </tt>
<a name="L5"></a><tt class="py-lineno">   5</tt>  <tt class="py-line"><tt class="py-comment">#              uncertainty analyses for simulation models.</tt> </tt>
<a name="L6"></a><tt class="py-lineno">   6</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno">   7</tt>  <tt class="py-line"><tt class="py-comment"># Author:      Fl&#225;vio Code&#231;o Coelho</tt> </tt>
<a name="L8"></a><tt class="py-lineno">   8</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L9"></a><tt class="py-lineno">   9</tt>  <tt class="py-line"><tt class="py-comment"># Created:     2003/08/10</tt> </tt>
<a name="L10"></a><tt class="py-lineno">  10</tt>  <tt class="py-line"><tt class="py-comment"># Copyright:   (c) 2003-2010 by the Author</tt> </tt>
<a name="L11"></a><tt class="py-lineno">  11</tt>  <tt class="py-line"><tt class="py-comment"># Licence:     GPL v3</tt> </tt>
<a name="L12"></a><tt class="py-lineno">  12</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L13"></a><tt class="py-lineno">  13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">cPickle</tt> <tt class="py-keyword">as</tt> <tt class="py-name">CP</tt> </tt>
<a name="L14"></a><tt class="py-lineno">  14</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">copy</tt> </tt>
<a name="L15"></a><tt class="py-lineno">  15</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L16"></a><tt class="py-lineno">  16</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sqlite3</tt> </tt>
<a name="L17"></a><tt class="py-lineno">  17</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L18"></a><tt class="py-lineno">  18</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">xmlrpclib</tt> </tt>
<a name="L19"></a><tt class="py-lineno">  19</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">multiprocessing</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Pool</tt> </tt>
<a name="L20"></a><tt class="py-lineno">  20</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">time</tt> <tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L21"></a><tt class="py-lineno">  21</tt>  <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno">  22</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L23"></a><tt class="py-lineno">  23</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">as</tt> <tt class="py-name">P</tt> </tt>
<a name="L24"></a><tt class="py-lineno">  24</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt><tt class="py-op">,</tt> <tt class="py-name">ones</tt><tt class="py-op">,</tt> <tt class="py-name">mean</tt><tt class="py-op">,</tt> <tt class="py-name">var</tt><tt class="py-op">,</tt> <tt class="py-name">sqrt</tt><tt class="py-op">,</tt> <tt class="py-name">floor</tt><tt class="py-op">,</tt> <tt class="py-name">isnan</tt><tt class="py-op">,</tt>  <tt class="py-name">nansum</tt><tt class="py-op">,</tt> <tt class="py-name">median</tt> </tt>
<a name="L25"></a><tt class="py-lineno">  25</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">core</tt><tt class="py-op">.</tt><tt class="py-name">records</tt> <tt class="py-keyword">import</tt> <tt class="py-name">recarray</tt> </tt>
<a name="L26"></a><tt class="py-lineno">  26</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">randint</tt><tt class="py-op">,</tt> <tt class="py-name">random</tt><tt class="py-op">,</tt> <tt class="py-name">seed</tt> </tt>
<a name="L27"></a><tt class="py-lineno">  27</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">stats</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel.optimize()=trunk.BIP.Bayes.Melding.FitModel-class.html#optimize"><a title="trunk.BIP.Bayes.Melding.FitModel.optimize" class="py-name" href="#" onclick="return doclink('link-0', 'optimize', 'link-0');">optimize</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">optim</tt> </tt>
<a name="L28"></a><tt class="py-lineno">  28</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt> <tt class="py-keyword">import</tt> <tt class="py-name">nanmean</tt> </tt>
<a name="L29"></a><tt class="py-lineno">  29</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">kde</tt> <tt class="py-keyword">import</tt> <tt class="py-name">gaussian_kde</tt> </tt>
<a name="L30"></a><tt class="py-lineno">  30</tt>  <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno">  31</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module trunk.BIP.Bayes.PlotMeld=trunk.BIP.Bayes.PlotMeld-module.html"><a title="trunk.BIP.Bayes.PlotMeld" class="py-name" href="#" onclick="return doclink('link-1', 'PlotMeld', 'link-1');">PlotMeld</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">PM</tt> </tt>
<a name="L32"></a><tt class="py-lineno">  32</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module trunk.BIP.Bayes.lhs=trunk.BIP.Bayes.lhs-module.html,Function trunk.BIP.Bayes.lhs.lhs()=trunk.BIP.Bayes.lhs-module.html#lhs"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-2', 'lhs', 'link-2');">lhs</a></tt> </tt>
<a name="L33"></a><tt class="py-lineno">  33</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module trunk.BIP.Bayes.like=trunk.BIP.Bayes.like-module.html"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-3', 'like', 'link-3');">like</a></tt> </tt>
<a name="L34"></a><tt class="py-lineno">  34</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Package trunk.BIP=trunk.BIP-module.html"><a title="trunk.BIP" class="py-name" href="#" onclick="return doclink('link-4', 'BIP', 'link-4');">BIP</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package trunk.BIP.Bayes=trunk.BIP.Bayes-module.html"><a title="trunk.BIP.Bayes" class="py-name" href="#" onclick="return doclink('link-5', 'Bayes', 'link-5');">Bayes</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Package trunk.BIP.Bayes.Samplers=trunk.BIP.Bayes.Samplers-module.html"><a title="trunk.BIP.Bayes.Samplers" class="py-name" href="#" onclick="return doclink('link-6', 'Samplers', 'link-6');">Samplers</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Module trunk.BIP.Bayes.Samplers.MCMC=trunk.BIP.Bayes.Samplers.MCMC-module.html"><a title="trunk.BIP.Bayes.Samplers.MCMC" class="py-name" href="#" onclick="return doclink('link-7', 'MCMC', 'link-7');">MCMC</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno">  35</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pdb</tt> </tt>
<a name="L36"></a><tt class="py-lineno">  36</tt>  <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno">  37</tt>  <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno">  38</tt>  <tt class="py-line"><tt class="py-comment">#try:</tt> </tt>
<a name="L39"></a><tt class="py-lineno">  39</tt>  <tt class="py-line"><tt class="py-comment">#    import psyco</tt> </tt>
<a name="L40"></a><tt class="py-lineno">  40</tt>  <tt class="py-line"><tt class="py-comment">#    psyco.full()</tt> </tt>
<a name="L41"></a><tt class="py-lineno">  41</tt>  <tt class="py-line"><tt class="py-comment">#except:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">  42</tt>  <tt class="py-line"><tt class="py-comment">#    pass</tt> </tt>
<a name="L43"></a><tt class="py-lineno">  43</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno">  44</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-8" class="py-name"><a title="trunk.BIP" class="py-name" href="#" onclick="return doclink('link-8', 'BIP', 'link-4');">BIP</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Variable trunk.BIP.Bayes.Melding.Viz=trunk.BIP.Bayes.Melding-module.html#Viz,Package trunk.BIP.Viz=trunk.BIP.Viz-module.html"><a title="trunk.BIP.Bayes.Melding.Viz
trunk.BIP.Viz" class="py-name" href="#" onclick="return doclink('link-9', 'Viz', 'link-9');">Viz</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Module trunk.BIP.Viz.realtime=trunk.BIP.Viz.realtime-module.html"><a title="trunk.BIP.Viz.realtime" class="py-name" href="#" onclick="return doclink('link-10', 'realtime', 'link-10');">realtime</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Class trunk.BIP.Viz.realtime.RTplot=trunk.BIP.Viz.realtime.RTplot-class.html"><a title="trunk.BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-11', 'RTplot', 'link-11');">RTplot</a></tt> </tt>
<a name="L45"></a><tt class="py-lineno">  45</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">liveplots</tt><tt class="py-op">.</tt><tt class="py-name">xmlrpcserver</tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Function trunk.BIP.Viz.realtime.rpc_plot()=trunk.BIP.Viz.realtime-module.html#rpc_plot"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-12', 'rpc_plot', 'link-12');">rpc_plot</a></tt> </tt>
<a name="L46"></a><tt class="py-lineno">  46</tt>  <tt class="py-line">    <tt id="link-13" class="py-name"><a title="trunk.BIP.Bayes.Melding.Viz
trunk.BIP.Viz" class="py-name" href="#" onclick="return doclink('link-13', 'Viz', 'link-9');">Viz</a></tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L47"></a><tt class="py-lineno">  47</tt>  <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno">  48</tt>  <tt class="py-line">    <tt id="link-14" class="py-name"><a title="trunk.BIP.Bayes.Melding.Viz
trunk.BIP.Viz" class="py-name" href="#" onclick="return doclink('link-14', 'Viz', 'link-9');">Viz</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt> </tt>
<a name="L49"></a><tt class="py-lineno">  49</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">r"""Please install Gnuplot-py to enable realtime visualization.</tt> </tt>
<a name="L50"></a><tt class="py-lineno">  50</tt>  <tt class="py-line"><tt class="py-string">    http://gnuplot-py.sourceforge.net/</tt> </tt>
<a name="L51"></a><tt class="py-lineno">  51</tt>  <tt class="py-line"><tt class="py-string">    """</tt> </tt>
<a name="L52"></a><tt class="py-lineno">  52</tt>  <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno">  53</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt id="link-15" class="py-name"><a title="trunk.BIP.Bayes.Melding.Viz
trunk.BIP.Viz" class="py-name" href="#" onclick="return doclink('link-15', 'Viz', 'link-9');">Viz</a></tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno">  54</tt>  <tt class="py-line">    <tt id="link-16" class="py-name" targets="Variable trunk.BIP.Bayes.Melding.dtplot=trunk.BIP.Bayes.Melding-module.html#dtplot"><a title="trunk.BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-16', 'dtplot', 'link-16');">dtplot</a></tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-17', 'RTplot', 'link-11');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-18" class="py-name" targets="Variable trunk.BIP.Bayes.Melding.phiplot=trunk.BIP.Bayes.Melding-module.html#phiplot"><a title="trunk.BIP.Bayes.Melding.phiplot" class="py-name" href="#" onclick="return doclink('link-18', 'phiplot', 'link-18');">phiplot</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-19', 'RTplot', 'link-11');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-20" class="py-name" targets="Variable trunk.BIP.Bayes.Melding.thplot=trunk.BIP.Bayes.Melding-module.html#thplot"><a title="trunk.BIP.Bayes.Melding.thplot" class="py-name" href="#" onclick="return doclink('link-20', 'thplot', 'link-20');">thplot</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-21', 'RTplot', 'link-11');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">  55</tt>  <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno">  56</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L57"></a><tt class="py-lineno">  57</tt>  <tt class="py-line"> </tt>
<a name="FitModel"></a><div id="FitModel-def"><a name="L58"></a><tt class="py-lineno">  58</tt> <a class="py-toggle" href="#" id="FitModel-toggle" onclick="return toggle('FitModel');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html">FitModel</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="FitModel-expanded"><a name="L59"></a><tt class="py-lineno">  59</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L60"></a><tt class="py-lineno">  60</tt>  <tt class="py-line"><tt class="py-docstring">    Fit a model to data generating</tt> </tt>
<a name="L61"></a><tt class="py-lineno">  61</tt>  <tt class="py-line"><tt class="py-docstring">    Bayesian posterior distributions of input and</tt> </tt>
<a name="L62"></a><tt class="py-lineno">  62</tt>  <tt class="py-line"><tt class="py-docstring">    outputs of the model.</tt> </tt>
<a name="L63"></a><tt class="py-lineno">  63</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="FitModel.__init__"></a><div id="FitModel.__init__-def"><a name="L64"></a><tt class="py-lineno">  64</tt> <a class="py-toggle" href="#" id="FitModel.__init__-toggle" onclick="return toggle('FitModel.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">K</tt><tt class="py-op">,</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">inits</tt><tt class="py-op">,</tt><tt class="py-param">tf</tt><tt class="py-op">,</tt><tt class="py-param">thetanames</tt><tt class="py-op">,</tt><tt class="py-param">phinames</tt><tt class="py-op">,</tt><tt class="py-param">wl</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-op">,</tt><tt class="py-param">nw</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">verbose</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-param">burnin</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">,</tt> <tt class="py-param">constraints</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.__init__-expanded"><a name="L65"></a><tt class="py-lineno">  65</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L66"></a><tt class="py-lineno">  66</tt>  <tt class="py-line"><tt class="py-docstring">        Initialize the model fitter.</tt> </tt>
<a name="L67"></a><tt class="py-lineno">  67</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L68"></a><tt class="py-lineno">  68</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L69"></a><tt class="py-lineno">  69</tt>  <tt class="py-line"><tt class="py-docstring">            - `K`: Number of samples from the priors. On MCMC also the number of samples of the posterior.</tt> </tt>
<a name="L70"></a><tt class="py-lineno">  70</tt>  <tt class="py-line"><tt class="py-docstring">            - `model`: Callable (function) returning the output of the model, from a set of parameter values received as argument.</tt> </tt>
<a name="L71"></a><tt class="py-lineno">  71</tt>  <tt class="py-line"><tt class="py-docstring">            - `inits`: inits initial values for the model's variables.</tt> </tt>
<a name="L72"></a><tt class="py-lineno">  72</tt>  <tt class="py-line"><tt class="py-docstring">            - `tf`: Length of the simulation, in units of time.</tt> </tt>
<a name="L73"></a><tt class="py-lineno">  73</tt>  <tt class="py-line"><tt class="py-docstring">            - `phinames`: List of names (strings) with names of the model's variables</tt> </tt>
<a name="L74"></a><tt class="py-lineno">  74</tt>  <tt class="py-line"><tt class="py-docstring">            - `thetanames`: List of names (strings) with names of parameters included on the inference.</tt> </tt>
<a name="L75"></a><tt class="py-lineno">  75</tt>  <tt class="py-line"><tt class="py-docstring">            - `wl`: window lenght length of the inference window.</tt> </tt>
<a name="L76"></a><tt class="py-lineno">  76</tt>  <tt class="py-line"><tt class="py-docstring">            - `nw`: Number of windows to analyze on iterative inference mode</tt> </tt>
<a name="L77"></a><tt class="py-lineno">  77</tt>  <tt class="py-line"><tt class="py-docstring">            - `verbose`: Verbosity level: 0, 1 or 2.</tt> </tt>
<a name="L78"></a><tt class="py-lineno">  78</tt>  <tt class="py-line"><tt class="py-docstring">            - `burnin`: number of burnin samples, used in the case on mcmc method.</tt> </tt>
<a name="L79"></a><tt class="py-lineno">  79</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L80"></a><tt class="py-lineno">  80</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno">  81</tt>  <tt class="py-line">            <tt class="py-keyword">assert</tt> <tt class="py-name">wl</tt><tt class="py-op">&lt;=</tt><tt class="py-name">tf</tt> </tt>
<a name="L82"></a><tt class="py-lineno">  82</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno">  83</tt>  <tt class="py-line">           <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">"Window Length cannot be larger that Length of the simulation(tf)"</tt> <tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno">  84</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">constraints</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno">  85</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt> <tt class="py-op">=</tt> <tt class="py-name">K</tt> </tt>
<a name="L86"></a><tt class="py-lineno">  86</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt> <tt class="py-op">=</tt> <tt class="py-number">.1</tt><tt class="py-op">*</tt><tt class="py-name">K</tt> <tt class="py-keyword">if</tt> <tt class="py-name">K</tt><tt class="py-op">&gt;</tt><tt class="py-number">2000</tt> <tt class="py-keyword">else</tt> <tt class="py-name">K</tt> </tt>
<a name="L87"></a><tt class="py-lineno">  87</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">finits</tt> <tt class="py-op">=</tt> <tt class="py-name">inits</tt> <tt class="py-comment">#first initial values</tt> </tt>
<a name="L88"></a><tt class="py-lineno">  88</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ftf</tt> <tt class="py-op">=</tt> <tt class="py-name">tf</tt> </tt>
<a name="L89"></a><tt class="py-lineno">  89</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">full_len</tt> <tt class="py-op">=</tt>  <tt class="py-name">wl</tt><tt class="py-op">*</tt><tt class="py-name">nw</tt> <tt class="py-keyword">if</tt> <tt class="py-name">wl</tt> <tt class="py-op">!=</tt><tt class="py-name">None</tt> <tt class="py-keyword">else</tt> <tt class="py-name">tf</tt> </tt>
<a name="L90"></a><tt class="py-lineno">  90</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> <tt class="py-op">=</tt> <tt class="py-name">inits</tt> </tt>
<a name="L91"></a><tt class="py-lineno">  91</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt> <tt class="py-op">=</tt> <tt class="py-name">tf</tt> </tt>
<a name="L92"></a><tt class="py-lineno">  92</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ew</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment">#expanding windows?</tt> </tt>
<a name="L93"></a><tt class="py-lineno">  93</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">totpop</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">inits</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno">  94</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Function trunk.BIP.Bayes.Melding.model()=trunk.BIP.Bayes.Melding-module.html#model"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-22', 'model', 'link-22');">model</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-23', 'model', 'link-22');">model</a></tt> </tt>
<a name="L95"></a><tt class="py-lineno">  95</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">phinames</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno">  96</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">thetanames</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno">  97</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt> <tt class="py-op">=</tt> <tt class="py-name">phinames</tt> </tt>
<a name="L98"></a><tt class="py-lineno">  98</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt> <tt class="py-op">=</tt> <tt class="py-name">thetanames</tt> </tt>
<a name="L99"></a><tt class="py-lineno">  99</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-24', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'inits'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> </tt>
<a name="L100"></a><tt class="py-lineno"> 100</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-25', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'tf'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt> </tt>
<a name="L101"></a><tt class="py-lineno"> 101</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-26', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'thetanames'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt> </tt>
<a name="L102"></a><tt class="py-lineno"> 102</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> <tt class="py-op">=</tt> <tt class="py-name">wl</tt> </tt>
<a name="L103"></a><tt class="py-lineno"> 103</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt> <tt class="py-op">=</tt> <tt class="py-name">nw</tt> </tt>
<a name="L104"></a><tt class="py-lineno"> 104</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L105"></a><tt class="py-lineno"> 105</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prior_set</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L106"></a><tt class="py-lineno"> 106</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt> <tt class="py-op">=</tt> <tt class="py-name">burnin</tt> </tt>
<a name="L107"></a><tt class="py-lineno"> 107</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">=</tt> <tt class="py-name">verbose</tt> </tt>
<a name="L108"></a><tt class="py-lineno"> 108</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">constraints</tt> <tt class="py-op">=</tt> <tt class="py-name">constraints</tt> </tt>
<a name="L109"></a><tt class="py-lineno"> 109</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pool</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> <tt class="py-comment">#this will be updated by the run method.</tt> </tt>
<a name="L110"></a><tt class="py-lineno"> 110</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Class trunk.BIP.Bayes.Melding.Meld=trunk.BIP.Bayes.Melding.Meld-class.html"><a title="trunk.BIP.Bayes.Melding.Meld" class="py-name" href="#" onclick="return doclink('link-27', 'Meld', 'link-27');">Meld</a></tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">L</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt id="link-28" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-28', 'model', 'link-22');">model</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-29', 'model', 'link-22');">model</a></tt><tt class="py-op">,</tt><tt class="py-name">ntheta</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">,</tt><tt class="py-name">nphi</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt><tt class="py-name">verbose</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno"> 111</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L112"></a><tt class="py-lineno"> 112</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L113"></a><tt class="py-lineno"> 113</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#DIC"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-30', 'DIC', 'link-30');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L114"></a><tt class="py-lineno"> 114</tt>  <tt class="py-line">        <tt class="py-comment"># To be defined by self.set.priors</tt> </tt>
<a name="L115"></a><tt class="py-lineno"> 115</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdists</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L116"></a><tt class="py-lineno"> 116</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ppars</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L117"></a><tt class="py-lineno"> 117</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plims</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L118"></a><tt class="py-lineno"> 118</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tdists</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L119"></a><tt class="py-lineno"> 119</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tpars</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L120"></a><tt class="py-lineno"> 120</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L121"></a><tt class="py-lineno"> 121</tt>  <tt class="py-line"> </tt>
<a name="FitModel._plot_MAP"></a><div id="FitModel._plot_MAP-def"><a name="L122"></a><tt class="py-lineno"> 122</tt> <a class="py-toggle" href="#" id="FitModel._plot_MAP-toggle" onclick="return toggle('FitModel._plot_MAP');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_plot_MAP">_plot_MAP</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">pmap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._plot_MAP-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._plot_MAP-expanded"><a name="L123"></a><tt class="py-lineno"> 123</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L124"></a><tt class="py-lineno"> 124</tt>  <tt class="py-line"><tt class="py-docstring">        Generates a plot of a full run of the model parameterized with the maximum a posteriori</tt> </tt>
<a name="L125"></a><tt class="py-lineno"> 125</tt>  <tt class="py-line"><tt class="py-docstring">        estimates of the parameters.</tt> </tt>
<a name="L126"></a><tt class="py-lineno"> 126</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L127"></a><tt class="py-lineno"> 127</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L128"></a><tt class="py-lineno"> 128</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: data dictionary as passed to optimize</tt> </tt>
<a name="L129"></a><tt class="py-lineno"> 129</tt>  <tt class="py-line"><tt class="py-docstring">            - `pmap`: MAP parameter values</tt> </tt>
<a name="L130"></a><tt class="py-lineno"> 130</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L131"></a><tt class="py-lineno"> 131</tt>  <tt class="py-line">        <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-31', 'RTplot', 'link-11');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-name">persist</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno"> 132</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-32', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'inits'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">finits</tt><tt class="py-op">;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-33', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'tf'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">full_len</tt> </tt>
<a name="L133"></a><tt class="py-lineno"> 133</tt>  <tt class="py-line">        <tt class="py-name">simseries</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-34', 'model', 'link-22');">model</a></tt><tt class="py-op">(</tt><tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">pmap</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno"> 134</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-35', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'inits'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-36', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'tf'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt> </tt>
<a name="L135"></a><tt class="py-lineno"> 135</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">'time'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno"> 136</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">pop</tt><tt class="py-op">(</tt><tt class="py-string">'time'</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno"> 137</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno"> 138</tt>  <tt class="py-line">            <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method trunk.BIP.Viz.realtime.RTplot.plotlines()=trunk.BIP.Viz.realtime.RTplot-class.html#plotlines,Method trunk.BIP.Viz.realtime.RTpyplot.plotlines()=trunk.BIP.Viz.realtime.RTpyplot-class.html#plotlines"><a title="trunk.BIP.Viz.realtime.RTplot.plotlines
trunk.BIP.Viz.realtime.RTpyplot.plotlines" class="py-name" href="#" onclick="return doclink('link-37', 'plotlines', 'link-37');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-string">'Obs. %s'</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-string">'points'</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno"> 139</tt>  <tt class="py-line">            <tt class="py-name">v</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno"> 140</tt>  <tt class="py-line">            <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.plotlines
trunk.BIP.Viz.realtime.RTpyplot.plotlines" class="py-name" href="#" onclick="return doclink('link-38', 'plotlines', 'link-37');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">simseries</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">[</tt><tt class="py-name">v</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Simulation with MAP parameters %s=%s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">,</tt><tt class="py-name">pmap</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L141"></a><tt class="py-lineno"> 141</tt>  <tt class="py-line"> </tt>
<a name="FitModel.AIC_from_RSS"></a><div id="FitModel.AIC_from_RSS-def"><a name="L142"></a><tt class="py-lineno"> 142</tt> <a class="py-toggle" href="#" id="FitModel.AIC_from_RSS-toggle" onclick="return toggle('FitModel.AIC_from_RSS');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#AIC_from_RSS">AIC_from_RSS</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.AIC_from_RSS-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.AIC_from_RSS-expanded"><a name="L143"></a><tt class="py-lineno"> 143</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L144"></a><tt class="py-lineno"> 144</tt>  <tt class="py-line"><tt class="py-docstring">        Calculates the Akaike information criterion from the residual sum of squares </tt> </tt>
<a name="L145"></a><tt class="py-lineno"> 145</tt>  <tt class="py-line"><tt class="py-docstring">        of the best fitting run.</tt> </tt>
<a name="L146"></a><tt class="py-lineno"> 146</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L147"></a><tt class="py-lineno"> 147</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="L148"></a><tt class="py-lineno"> 148</tt>  <tt class="py-line"> </tt>
<a name="FitModel.optimize"></a><div id="FitModel.optimize-def"><a name="L149"></a><tt class="py-lineno"> 149</tt> <a class="py-toggle" href="#" id="FitModel.optimize-toggle" onclick="return toggle('FitModel.optimize');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#optimize">optimize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">p0</tt><tt class="py-op">,</tt> <tt class="py-param">optimizer</tt><tt class="py-op">=</tt><tt class="py-string">'scipy'</tt><tt class="py-op">,</tt> <tt class="py-param">tol</tt><tt class="py-op">=</tt><tt class="py-number">0.0001</tt><tt class="py-op">,</tt> <tt class="py-param">verbose</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">plot</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.optimize-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.optimize-expanded"><a name="L150"></a><tt class="py-lineno"> 150</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L151"></a><tt class="py-lineno"> 151</tt>  <tt class="py-line"><tt class="py-docstring">        Finds best parameters using an optimization approach</tt> </tt>
<a name="L152"></a><tt class="py-lineno"> 152</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L153"></a><tt class="py-lineno"> 153</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L154"></a><tt class="py-lineno"> 154</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Dictionary of observed series</tt> </tt>
<a name="L155"></a><tt class="py-lineno"> 155</tt>  <tt class="py-line"><tt class="py-docstring">            - `p0`: Sequence (list or tuple) of initial values for the parameters</tt> </tt>
<a name="L156"></a><tt class="py-lineno"> 156</tt>  <tt class="py-line"><tt class="py-docstring">            - `optimizer`: Optimization library to use: 'scipy': fmin (Nelder-Mead) or 'oo':OpenOpt.NLP</tt> </tt>
<a name="L157"></a><tt class="py-lineno"> 157</tt>  <tt class="py-line"><tt class="py-docstring">            - `tol`: Tolerance of the error</tt> </tt>
<a name="L158"></a><tt class="py-lineno"> 158</tt>  <tt class="py-line"><tt class="py-docstring">            - `verbose`: If true show stats of the optimization run at the end</tt> </tt>
<a name="L159"></a><tt class="py-lineno"> 159</tt>  <tt class="py-line"><tt class="py-docstring">            - `plot`: If true plots a run based on the optimized parameters.</tt> </tt>
<a name="L160"></a><tt class="py-lineno"> 160</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L161"></a><tt class="py-lineno"> 161</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno"> 162</tt>  <tt class="py-line">            <tt class="py-keyword">import</tt> <tt class="py-name">openopt</tt> </tt>
<a name="L163"></a><tt class="py-lineno"> 163</tt>  <tt class="py-line">            <tt class="py-name">oo</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L164"></a><tt class="py-lineno"> 164</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno"> 165</tt>  <tt class="py-line">            <tt class="py-name">oo</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L166"></a><tt class="py-lineno"> 166</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">p0</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">list</tt><tt class="py-op">,</tt><tt class="py-name">tuple</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno"> 167</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">mse</tt><tt class="py-op">(</tt><tt class="py-param">theta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno"> 168</tt>  <tt class="py-line">            <tt class="py-name">s1</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name" targets="Function trunk.BIP.Bayes.Melding.model_as_ra()=trunk.BIP.Bayes.Melding-module.html#model_as_ra,Function trunk.BIP.Bayes.Samplers.MCMC.model_as_ra()=trunk.BIP.Bayes.Samplers.MCMC-module.html#model_as_ra"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-39', 'model_as_ra', 'link-39');">model_as_ra</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt>  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-40', 'model', 'link-22');">model</a></tt><tt class="py-op">,</tt>  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno"> 169</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._rms_error()=trunk.BIP.Bayes.Melding.FitModel-class.html#_rms_error"><a title="trunk.BIP.Bayes.Melding.FitModel._rms_error" class="py-name" href="#" onclick="return doclink('link-41', '_rms_error', 'link-41');">_rms_error</a></tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
</div><a name="L170"></a><tt class="py-lineno"> 170</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">optimizer</tt> <tt class="py-op">==</tt> <tt class="py-string">"scipy"</tt><tt class="py-op">:</tt> </tt>
<a name="L171"></a><tt class="py-lineno"> 171</tt>  <tt class="py-line">            <tt class="py-name">potimo</tt> <tt class="py-op">=</tt> <tt class="py-name">optim</tt><tt class="py-op">.</tt><tt class="py-name">fmin</tt><tt class="py-op">(</tt><tt class="py-name">mse</tt><tt class="py-op">,</tt><tt class="py-name">p0</tt><tt class="py-op">,</tt><tt class="py-name">ftol</tt><tt class="py-op">=</tt><tt class="py-name">tol</tt><tt class="py-op">,</tt> <tt class="py-name">disp</tt><tt class="py-op">=</tt><tt class="py-name">verbose</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno"> 172</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">optimizer</tt> <tt class="py-op">==</tt> <tt class="py-string">"oo"</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno"> 173</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">oo</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno"> 174</tt>  <tt class="py-line">                <tt class="py-name">potimo</tt> <tt class="py-op">=</tt> <tt class="py-name">optim</tt><tt class="py-op">.</tt><tt class="py-name">fmin</tt><tt class="py-op">(</tt><tt class="py-name">mse</tt><tt class="py-op">,</tt><tt class="py-name">p0</tt><tt class="py-op">,</tt><tt class="py-name">ftol</tt><tt class="py-op">=</tt><tt class="py-name">tol</tt><tt class="py-op">,</tt> <tt class="py-name">disp</tt><tt class="py-op">=</tt><tt class="py-name">verbose</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno"> 175</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt>  </tt>
<a name="L176"></a><tt class="py-lineno"> 176</tt>  <tt class="py-line">                <tt class="py-name">lb</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt> <tt class="py-keyword">else</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno"> 177</tt>  <tt class="py-line">                <tt class="py-name">ub</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt> <tt class="py-keyword">else</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno"> 178</tt>  <tt class="py-line">                <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">openopt</tt><tt class="py-op">.</tt><tt class="py-name">NLP</tt><tt class="py-op">(</tt><tt class="py-name">mse</tt><tt class="py-op">,</tt> <tt class="py-name">p0</tt><tt class="py-op">,</tt> <tt class="py-name">lb</tt><tt class="py-op">=</tt><tt class="py-name">lb</tt><tt class="py-op">,</tt> <tt class="py-name">ub</tt><tt class="py-op">=</tt><tt class="py-name">ub</tt><tt class="py-op">,</tt> <tt class="py-name">ftol</tt><tt class="py-op">=</tt><tt class="py-name">tol</tt><tt class="py-op">,</tt> <tt class="py-name">iprint</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno"> 179</tt>  <tt class="py-line">                <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">solve</tt><tt class="py-op">(</tt><tt class="py-string">'ralg'</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno"> 180</tt>  <tt class="py-line">                <tt class="py-name">potimo</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xf</tt> </tt>
<a name="L181"></a><tt class="py-lineno"> 181</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt><tt class="py-comment">#use fmin as fallback method</tt> </tt>
<a name="L182"></a><tt class="py-lineno"> 182</tt>  <tt class="py-line">            <tt class="py-name">potimo</tt> <tt class="py-op">=</tt> <tt class="py-name">optim</tt><tt class="py-op">.</tt><tt class="py-name">fmin</tt><tt class="py-op">(</tt><tt class="py-name">mse</tt><tt class="py-op">,</tt><tt class="py-name">p0</tt><tt class="py-op">,</tt><tt class="py-name">ftol</tt><tt class="py-op">=</tt><tt class="py-name">tol</tt><tt class="py-op">,</tt> <tt class="py-name">disp</tt><tt class="py-op">=</tt><tt class="py-name">verbose</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno"> 183</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">plot</tt><tt class="py-op">:</tt> </tt>
<a name="L184"></a><tt class="py-lineno"> 184</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._plot_MAP()=trunk.BIP.Bayes.Melding.FitModel-class.html#_plot_MAP"><a title="trunk.BIP.Bayes.Melding.FitModel._plot_MAP" class="py-name" href="#" onclick="return doclink('link-42', '_plot_MAP', 'link-42');">_plot_MAP</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">potimo</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno"> 185</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">potimo</tt> </tt>
</div><a name="L186"></a><tt class="py-lineno"> 186</tt>  <tt class="py-line">         </tt>
<a name="FitModel._rms_error"></a><div id="FitModel._rms_error-def"><a name="L187"></a><tt class="py-lineno"> 187</tt> <a class="py-toggle" href="#" id="FitModel._rms_error-toggle" onclick="return toggle('FitModel._rms_error');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_rms_error">_rms_error</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s1</tt><tt class="py-op">,</tt> <tt class="py-param">s2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._rms_error-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._rms_error-expanded"><a name="L188"></a><tt class="py-lineno"> 188</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L189"></a><tt class="py-lineno"> 189</tt>  <tt class="py-line"><tt class="py-docstring">        Calculates a the error between a model-</tt> </tt>
<a name="L190"></a><tt class="py-lineno"> 190</tt>  <tt class="py-line"><tt class="py-docstring">        generated time series and a observed time series.</tt> </tt>
<a name="L191"></a><tt class="py-lineno"> 191</tt>  <tt class="py-line"><tt class="py-docstring">        It uses a normalized RMS deviation.</tt> </tt>
<a name="L192"></a><tt class="py-lineno"> 192</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L193"></a><tt class="py-lineno"> 193</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L194"></a><tt class="py-lineno"> 194</tt>  <tt class="py-line"><tt class="py-docstring">            - `s1`: model-generated time series. </tt> </tt>
<a name="L195"></a><tt class="py-lineno"> 195</tt>  <tt class="py-line"><tt class="py-docstring">            - `s2`: observed time series. dictionary with keys matching names of s1</tt> </tt>
<a name="L196"></a><tt class="py-lineno"> 196</tt>  <tt class="py-line"><tt class="py-docstring">        :Types:</tt> </tt>
<a name="L197"></a><tt class="py-lineno"> 197</tt>  <tt class="py-line"><tt class="py-docstring">            - `s1`: Record array or list.</tt> </tt>
<a name="L198"></a><tt class="py-lineno"> 198</tt>  <tt class="py-line"><tt class="py-docstring">            - `s2`: Dictionary or list; must be a dictionary if s1 is a RA</tt> </tt>
<a name="L199"></a><tt class="py-lineno"> 199</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L200"></a><tt class="py-lineno"> 200</tt>  <tt class="py-line"><tt class="py-docstring">        s1 and s2 can also be both lists of lists or lists of arrays of the same length.</tt> </tt>
<a name="L201"></a><tt class="py-lineno"> 201</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L202"></a><tt class="py-lineno"> 202</tt>  <tt class="py-line"><tt class="py-docstring">        :Return:</tt> </tt>
<a name="L203"></a><tt class="py-lineno"> 203</tt>  <tt class="py-line"><tt class="py-docstring">            The Root mean square deviation between `s1` and `s2`.</tt> </tt>
<a name="L204"></a><tt class="py-lineno"> 204</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L205"></a><tt class="py-lineno"> 205</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">recarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno"> 206</tt>  <tt class="py-line">            <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno"> 207</tt>  <tt class="py-line">            <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L208"></a><tt class="py-lineno"> 208</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno"> 209</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">k</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s1</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno"> 210</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L211"></a><tt class="py-lineno"> 211</tt>  <tt class="py-line">                <tt class="py-name">ls1</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment">#handles the cases where data is slightly longer that simulated series.</tt> </tt>
<a name="L212"></a><tt class="py-lineno"> 212</tt>  <tt class="py-line"><tt class="py-comment">#                print s2[k]</tt> </tt>
<a name="L213"></a><tt class="py-lineno"> 213</tt>  <tt class="py-line"><tt class="py-comment">#                try:</tt> </tt>
<a name="L214"></a><tt class="py-lineno"> 214</tt>  <tt class="py-line"><tt class="py-comment">#                pdb.set_trace()</tt> </tt>
<a name="L215"></a><tt class="py-lineno"> 215</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno"> 216</tt>  <tt class="py-line">                    <tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno"> 217</tt>  <tt class="py-line">                <tt class="py-name">dif</tt> <tt class="py-op">=</tt> <tt class="py-name">s1</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">ls1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno"> 218</tt>  <tt class="py-line">                 </tt>
<a name="L219"></a><tt class="py-lineno"> 219</tt>  <tt class="py-line">                <tt class="py-name">dif</tt><tt class="py-op">[</tt><tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L220"></a><tt class="py-lineno"> 220</tt>  <tt class="py-line">                <tt id="link-43" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.e=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#e"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-43', 'e', 'link-43');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno"> 221</tt>  <tt class="py-line"><tt class="py-comment">#                except TypeError:</tt> </tt>
<a name="L222"></a><tt class="py-lineno"> 222</tt>  <tt class="py-line"><tt class="py-comment">#                    print s1[k], s2[k]</tt> </tt>
<a name="L223"></a><tt class="py-lineno"> 223</tt>  <tt class="py-line"> </tt>
<a name="L224"></a><tt class="py-lineno"> 224</tt>  <tt class="py-line">                <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-44', 'e', 'link-43');">e</a></tt><tt class="py-op">)</tt>  </tt>
<a name="L225"></a><tt class="py-lineno"> 225</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno"> 226</tt>  <tt class="py-line">            <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno"> 227</tt>  <tt class="py-line">            <tt class="py-name">s1</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno"> 228</tt>  <tt class="py-line">            <tt class="py-name">s2</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno"> 229</tt>  <tt class="py-line">            <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nanmean</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">s2</tt><tt class="py-op">)</tt> <tt class="py-op">]</tt> </tt>
<a name="L230"></a><tt class="py-lineno"> 230</tt>  <tt class="py-line">            <tt class="py-comment">#err = [sum((s-t)**2./t**2) for s, t in zip(s1, s2)]</tt> </tt>
<a name="L231"></a><tt class="py-lineno"> 231</tt>  <tt class="py-line">        <tt class="py-name">rmsd</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno"> 232</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">rmsd</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno"> 233</tt>  <tt class="py-line">         </tt>
<a name="FitModel.set_priors"></a><div id="FitModel.set_priors-def"><a name="L234"></a><tt class="py-lineno"> 234</tt> <a class="py-toggle" href="#" id="FitModel.set_priors-toggle" onclick="return toggle('FitModel.set_priors');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#set_priors">set_priors</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">tdists</tt><tt class="py-op">,</tt><tt class="py-param">tpars</tt><tt class="py-op">,</tt> <tt class="py-param">tlims</tt><tt class="py-op">,</tt><tt class="py-param">pdists</tt><tt class="py-op">,</tt><tt class="py-param">ppars</tt><tt class="py-op">,</tt><tt class="py-param">plims</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.set_priors-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.set_priors-expanded"><a name="L235"></a><tt class="py-lineno"> 235</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L236"></a><tt class="py-lineno"> 236</tt>  <tt class="py-line"><tt class="py-docstring">        Set the prior distributions for Phi and Theta</tt> </tt>
<a name="L237"></a><tt class="py-lineno"> 237</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L238"></a><tt class="py-lineno"> 238</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L239"></a><tt class="py-lineno"> 239</tt>  <tt class="py-line"><tt class="py-docstring">            - `pdists`: distributions for the output variables. For example: [scipy.stats.uniform,scipy.stats.norm]</tt> </tt>
<a name="L240"></a><tt class="py-lineno"> 240</tt>  <tt class="py-line"><tt class="py-docstring">            - `ppars`: paramenters for the distributions in pdists. For example: [(0,1),(0,1)]</tt> </tt>
<a name="L241"></a><tt class="py-lineno"> 241</tt>  <tt class="py-line"><tt class="py-docstring">            - `plims`: Limits of the range of each phi. List of (min,max) tuples.</tt> </tt>
<a name="L242"></a><tt class="py-lineno"> 242</tt>  <tt class="py-line"><tt class="py-docstring">            - `tdists`: same as pdists, but for input parameters (Theta).</tt> </tt>
<a name="L243"></a><tt class="py-lineno"> 243</tt>  <tt class="py-line"><tt class="py-docstring">            - `tpars`: same as ppars, but for tdists.</tt> </tt>
<a name="L244"></a><tt class="py-lineno"> 244</tt>  <tt class="py-line"><tt class="py-docstring">            - `tlims`: Limits of the range of each theta. List of (min,max) tuples.</tt> </tt>
<a name="L245"></a><tt class="py-lineno"> 245</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L246"></a><tt class="py-lineno"> 246</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdists</tt> <tt class="py-op">=</tt> <tt class="py-name">pdists</tt> </tt>
<a name="L247"></a><tt class="py-lineno"> 247</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ppars</tt> <tt class="py-op">=</tt> <tt class="py-name">ppars</tt> </tt>
<a name="L248"></a><tt class="py-lineno"> 248</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plims</tt> <tt class="py-op">=</tt> <tt class="py-name">plims</tt> </tt>
<a name="L249"></a><tt class="py-lineno"> 249</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tdists</tt> <tt class="py-op">=</tt> <tt class="py-name">tdists</tt> </tt>
<a name="L250"></a><tt class="py-lineno"> 250</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tpars</tt> <tt class="py-op">=</tt> <tt class="py-name">tpars</tt> </tt>
<a name="L251"></a><tt class="py-lineno"> 251</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt> <tt class="py-op">=</tt> <tt class="py-name">tlims</tt> </tt>
<a name="L252"></a><tt class="py-lineno"> 252</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._init_priors()=trunk.BIP.Bayes.Melding.FitModel-class.html#_init_priors"><a title="trunk.BIP.Bayes.Melding.FitModel._init_priors" class="py-name" href="#" onclick="return doclink('link-45', '_init_priors', 'link-45');">_init_priors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno"> 253</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prior_set</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L254"></a><tt class="py-lineno"> 254</tt>  <tt class="py-line">     </tt>
<a name="FitModel.prior_sample"></a><div id="FitModel.prior_sample-def"><a name="L255"></a><tt class="py-lineno"> 255</tt> <a class="py-toggle" href="#" id="FitModel.prior_sample-toggle" onclick="return toggle('FitModel.prior_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#prior_sample">prior_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.prior_sample-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.prior_sample-expanded"><a name="L256"></a><tt class="py-lineno"> 256</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L257"></a><tt class="py-lineno"> 257</tt>  <tt class="py-line"><tt class="py-docstring">        Generates a set of sample from the starting theta prior distributions</tt> </tt>
<a name="L258"></a><tt class="py-lineno"> 258</tt>  <tt class="py-line"><tt class="py-docstring">        for reporting purposes.</tt> </tt>
<a name="L259"></a><tt class="py-lineno"> 259</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L260"></a><tt class="py-lineno"> 260</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L261"></a><tt class="py-lineno"> 261</tt>  <tt class="py-line"><tt class="py-docstring">            Dictionary with (name,sample) pairs</tt> </tt>
<a name="L262"></a><tt class="py-lineno"> 262</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L263"></a><tt class="py-lineno"> 263</tt>  <tt class="py-line">        <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L264"></a><tt class="py-lineno"> 264</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno"> 265</tt>  <tt class="py-line">            <tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tdists</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tpars</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno"> 266</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">s</tt> </tt>
</div><a name="L267"></a><tt class="py-lineno"> 267</tt>  <tt class="py-line">             </tt>
<a name="FitModel._init_priors"></a><div id="FitModel._init_priors-def"><a name="L268"></a><tt class="py-lineno"> 268</tt> <a class="py-toggle" href="#" id="FitModel._init_priors-toggle" onclick="return toggle('FitModel._init_priors');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_init_priors">_init_priors</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._init_priors-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._init_priors-expanded"><a name="L269"></a><tt class="py-lineno"> 269</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L270"></a><tt class="py-lineno"> 270</tt>  <tt class="py-line"><tt class="py-docstring">        Initialize priors either from distributions or previous posteriors</tt> </tt>
<a name="L271"></a><tt class="py-lineno"> 271</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L272"></a><tt class="py-lineno"> 272</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">prior</tt><tt class="py-op">!=</tt><tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'phi'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno"> 273</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.setThetaFromData()=trunk.BIP.Bayes.Melding.Meld-class.html#setThetaFromData"><a title="trunk.BIP.Bayes.Melding.Meld.setThetaFromData" class="py-name" href="#" onclick="return doclink('link-46', 'setThetaFromData', 'link-46');">setThetaFromData</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">,</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno"> 274</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.setPhiFromData()=trunk.BIP.Bayes.Melding.Meld-class.html#setPhiFromData"><a title="trunk.BIP.Bayes.Melding.Meld.setPhiFromData" class="py-name" href="#" onclick="return doclink('link-47', 'setPhiFromData', 'link-47');">setPhiFromData</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">,</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'phi'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plims</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno"> 275</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno"> 276</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"++++&gt;"</tt> </tt>
<a name="L277"></a><tt class="py-lineno"> 277</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.setTheta()=trunk.BIP.Bayes.Melding.Meld-class.html#setTheta"><a title="trunk.BIP.Bayes.Melding.Meld.setTheta" class="py-name" href="#" onclick="return doclink('link-48', 'setTheta', 'link-48');">setTheta</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tdists</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tpars</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlims</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno"> 278</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.setPhi()=trunk.BIP.Bayes.Melding.Meld-class.html#setPhi"><a title="trunk.BIP.Bayes.Melding.Meld.setPhi" class="py-name" href="#" onclick="return doclink('link-49', 'setPhi', 'link-49');">setPhi</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdists</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ppars</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plims</tt><tt class="py-op">)</tt> </tt>
</div><a name="L279"></a><tt class="py-lineno"> 279</tt>  <tt class="py-line">             </tt>
<a name="FitModel.do_inference"></a><div id="FitModel.do_inference-def"><a name="L280"></a><tt class="py-lineno"> 280</tt> <a class="py-toggle" href="#" id="FitModel.do_inference-toggle" onclick="return toggle('FitModel.do_inference');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#do_inference">do_inference</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">predlen</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">,</tt> <tt class="py-param">likvar</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.do_inference-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.do_inference-expanded"><a name="L281"></a><tt class="py-lineno"> 281</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L282"></a><tt class="py-lineno"> 282</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L283"></a><tt class="py-lineno"> 283</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="trunk.BIP.Bayes.Melding.FitModel._init_priors" class="py-name" href="#" onclick="return doclink('link-50', '_init_priors', 'link-45');">_init_priors</a></tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno"> 284</tt>  <tt class="py-line">        <tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L285"></a><tt class="py-lineno"> 285</tt>  <tt class="py-line">        <tt class="py-name">att</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L286"></a><tt class="py-lineno"> 286</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno"> 287</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">:</tt> </tt>
<a name="L288"></a><tt class="py-lineno"> 288</tt>  <tt class="py-line">                <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">pop</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno"> 289</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"SIR"</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno"> 290</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">succ</tt><tt class="py-op">:</tt> <tt class="py-comment">#run sir Until is able to get a fit</tt> </tt>
<a name="L291"></a><tt class="py-lineno"> 291</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'attempt #'</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> </tt>
<a name="L292"></a><tt class="py-lineno"> 292</tt>  <tt class="py-line">                <tt class="py-name">succ</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.sir()=trunk.BIP.Bayes.Melding.Meld-class.html#sir"><a title="trunk.BIP.Bayes.Melding.Meld.sir" class="py-name" href="#" onclick="return doclink('link-51', 'sir', 'link-51');">sir</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">variance</tt><tt class="py-op">=</tt><tt class="py-name">likvar</tt><tt class="py-op">,</tt><tt class="py-name">pool</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pool</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno"> 293</tt>  <tt class="py-line">                <tt class="py-name">att</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L294"></a><tt class="py-lineno"> 294</tt>  <tt class="py-line">            <tt id="link-52" class="py-name" targets="Variable trunk.BIP.SDE.example.pt=trunk.BIP.SDE.example-module.html#pt"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-52', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.getPosteriors()=trunk.BIP.Bayes.Melding.Meld-class.html#getPosteriors"><a title="trunk.BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-53', 'getPosteriors', 'link-53');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno"> 295</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"MCMC"</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno"> 296</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">succ</tt><tt class="py-op">:</tt> <tt class="py-comment">#run sir Until is able to get a fitd == "mcmc":</tt> </tt>
<a name="L297"></a><tt class="py-lineno"> 297</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'attempt #'</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> </tt>
<a name="L298"></a><tt class="py-lineno"> 298</tt>  <tt class="py-line">                <tt class="py-name">succ</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.mcmc_run()=trunk.BIP.Bayes.Melding.Meld-class.html#mcmc_run"><a title="trunk.BIP.Bayes.Melding.Meld.mcmc_run" class="py-name" href="#" onclick="return doclink('link-54', 'mcmc_run', 'link-54');">mcmc_run</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">,</tt><tt class="py-name">likvariance</tt><tt class="py-op">=</tt><tt class="py-name">likvar</tt><tt class="py-op">,</tt><tt class="py-name">burnin</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-string">'MH'</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno"> 299</tt>  <tt class="py-line">            <tt id="link-55" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-55', 'pt', 'link-52');">pt</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> </tt>
<a name="L300"></a><tt class="py-lineno"> 300</tt>  <tt class="py-line">            <tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> </tt>
<a name="L301"></a><tt class="py-lineno"> 301</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"DREAM"</tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno"> 302</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">succ</tt><tt class="py-op">:</tt> <tt class="py-comment">#run sir Until is able to get a fitd == "mcmc":</tt> </tt>
<a name="L303"></a><tt class="py-lineno"> 303</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'attempt #'</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> </tt>
<a name="L304"></a><tt class="py-lineno"> 304</tt>  <tt class="py-line">                <tt class="py-name">succ</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.mcmc_run" class="py-name" href="#" onclick="return doclink('link-56', 'mcmc_run', 'link-54');">mcmc_run</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">,</tt><tt class="py-name">likvariance</tt><tt class="py-op">=</tt><tt class="py-name">likvar</tt><tt class="py-op">,</tt><tt class="py-name">burnin</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt>  <tt class="py-name">method</tt><tt class="py-op">=</tt><tt class="py-string">'dream'</tt><tt class="py-op">,</tt> <tt class="py-name">constraints</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">constraints</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno"> 305</tt>  <tt class="py-line">            <tt id="link-57" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-57', 'pt', 'link-52');">pt</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> </tt>
<a name="L306"></a><tt class="py-lineno"> 306</tt>  <tt class="py-line">            <tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> </tt>
<a name="L307"></a><tt class="py-lineno"> 307</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"ABC"</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno"> 308</tt>  <tt class="py-line">            <tt class="py-comment">#TODO: allow passing of fitfun</tt> </tt>
<a name="L309"></a><tt class="py-lineno"> 309</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.abcRun()=trunk.BIP.Bayes.Melding.Meld-class.html#abcRun"><a title="trunk.BIP.Bayes.Melding.Meld.abcRun" class="py-name" href="#" onclick="return doclink('link-58', 'abcRun', 'link-58');">abcRun</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">fitfun</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">pool</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pool</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno"> 310</tt>  <tt class="py-line">            <tt id="link-59" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-59', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-60', 'getPosteriors', 'link-53');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno"> 311</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">stop_now</tt><tt class="py-op">:</tt> </tt>
<a name="L312"></a><tt class="py-lineno"> 312</tt>  <tt class="py-line">            <tt class="py-comment"># if fitting has been prematurely interrupted by user</tt> </tt>
<a name="L313"></a><tt class="py-lineno"> 313</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt> </tt>
<a name="L314"></a><tt class="py-lineno"> 314</tt>  <tt class="py-line">        <tt class="py-name">pp</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L315"></a><tt class="py-lineno"> 315</tt>  <tt class="py-line">        <tt class="py-comment"># TODO: figure out what to do by default with inits</tt> </tt>
<a name="L316"></a><tt class="py-lineno"> 316</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt> <tt class="py-op">&gt;</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adjinits</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ew</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno"> 317</tt>  <tt class="py-line">            <tt class="py-name">adiff</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">vn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno"> 318</tt>  <tt class="py-line">            <tt class="py-name">diff</tt> <tt class="py-op">=</tt> <tt class="py-name">adiff</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-comment">#sum errors for all oserved variables</tt> </tt>
<a name="L319"></a><tt class="py-lineno"> 319</tt>  <tt class="py-line">            <tt class="py-name">initind</tt> <tt class="py-op">=</tt> <tt class="py-name">diff</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">diff</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno"> 320</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">pp</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">initind</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">vn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">]</tt> </tt>
<a name="L321"></a><tt class="py-lineno"> 321</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno"> 322</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L323"></a><tt class="py-lineno"> 323</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">v</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt>  </tt>
<a name="L324"></a><tt class="py-lineno"> 324</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-61', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'inits'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> </tt>
<a name="L325"></a><tt class="py-lineno"> 325</tt>  <tt class="py-line">         </tt>
<a name="L326"></a><tt class="py-lineno"> 326</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">predlen</tt><tt class="py-op">:</tt> </tt>
<a name="L327"></a><tt class="py-lineno"> 327</tt>  <tt class="py-line">            <tt class="py-name">predseries</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-62', 'getPosteriors', 'link-53');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-name">predlen</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L328"></a><tt class="py-lineno"> 328</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-63" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-63', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt> <tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> </tt>
</div><a name="L329"></a><tt class="py-lineno"> 329</tt>  <tt class="py-line"> </tt>
<a name="FitModel._save_to_db"></a><div id="FitModel._save_to_db-def"><a name="L330"></a><tt class="py-lineno"> 330</tt> <a class="py-toggle" href="#" id="FitModel._save_to_db-toggle" onclick="return toggle('FitModel._save_to_db');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_save_to_db">_save_to_db</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._save_to_db-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._save_to_db-expanded"><a name="L331"></a><tt class="py-lineno"> 331</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L332"></a><tt class="py-lineno"> 332</tt>  <tt class="py-line"><tt class="py-docstring">        Saves data to a sqlite3 db.</tt> </tt>
<a name="L333"></a><tt class="py-lineno"> 333</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L334"></a><tt class="py-lineno"> 334</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L335"></a><tt class="py-lineno"> 335</tt>  <tt class="py-line"><tt class="py-docstring">            - `dbname`: name of the database file</tt> </tt>
<a name="L336"></a><tt class="py-lineno"> 336</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Data dictionary as created by `format_db_tables` method.</tt> </tt>
<a name="L337"></a><tt class="py-lineno"> 337</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L338"></a><tt class="py-lineno"> 338</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">row_generator</tt><tt class="py-op">(</tt><tt class="py-param">var</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L339"></a><tt class="py-lineno"> 339</tt>  <tt class="py-line">            <tt class="py-docstring">'''</tt> </tt>
<a name="L340"></a><tt class="py-lineno"> 340</tt>  <tt class="py-line"><tt class="py-docstring">            var is a dictionary.</tt> </tt>
<a name="L341"></a><tt class="py-lineno"> 341</tt>  <tt class="py-line"><tt class="py-docstring">            '''</tt> </tt>
<a name="L342"></a><tt class="py-lineno"> 342</tt>  <tt class="py-line"><tt class="py-comment">#            if isinstance(var, numpy.recarray):</tt> </tt>
<a name="L343"></a><tt class="py-lineno"> 343</tt>  <tt class="py-line"><tt class="py-comment">#                for repl in var:</tt> </tt>
<a name="L344"></a><tt class="py-lineno"> 344</tt>  <tt class="py-line"><tt class="py-comment">#                    if isinstance(repl, numpy.recarray): # this is the case of variables, where each replicate is a time series</tt> </tt>
<a name="L345"></a><tt class="py-lineno"> 345</tt>  <tt class="py-line"><tt class="py-comment">#                        for t in repl:</tt> </tt>
<a name="L346"></a><tt class="py-lineno"> 346</tt>  <tt class="py-line"><tt class="py-comment">#                            if not isinstance(t, numpy.core.records.record):</tt> </tt>
<a name="L347"></a><tt class="py-lineno"> 347</tt>  <tt class="py-line"><tt class="py-comment">#                                t=(t,)</tt> </tt>
<a name="L348"></a><tt class="py-lineno"> 348</tt>  <tt class="py-line"><tt class="py-comment">#                            yield tuple(t) #variable tuple at time t in replicate repl</tt> </tt>
<a name="L349"></a><tt class="py-lineno"> 349</tt>  <tt class="py-line"><tt class="py-comment">#                    else: #this is the case of parameters</tt> </tt>
<a name="L350"></a><tt class="py-lineno"> 350</tt>  <tt class="py-line"><tt class="py-comment">#                        yield tuple(repl)</tt> </tt>
<a name="L351"></a><tt class="py-lineno"> 351</tt>  <tt class="py-line"><tt class="py-comment">#            elif isinstance(var, dict):</tt> </tt>
<a name="L352"></a><tt class="py-lineno"> 352</tt>  <tt class="py-line"><tt class="py-comment">#                try:</tt> </tt>
<a name="L353"></a><tt class="py-lineno"> 353</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-64" class="py-name" targets="Variable trunk.BIP.SDE.example.r=trunk.BIP.SDE.example-module.html#r"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-64', 'r', 'link-64');">r</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">var</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno"> 354</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-65', 'r', 'link-64');">r</a></tt><tt class="py-op">,</tt> <tt class="py-name">tuple</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno"> 355</tt>  <tt class="py-line">                    <tt id="link-66" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-66', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-67', 'r', 'link-64');">r</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno"> 356</tt>  <tt class="py-line">                <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L357"></a><tt class="py-lineno"> 357</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt id="link-68" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-68', 'r', 'link-64');">r</a></tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno"> 358</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno"> 359</tt>  <tt class="py-line">                        <tt class="py-name">t</tt><tt class="py-op">+=</tt><tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno"> 360</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L361"></a><tt class="py-lineno"> 361</tt>  <tt class="py-line">                        <tt class="py-name">t</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L362"></a><tt class="py-lineno"> 362</tt>  <tt class="py-line">                    <tt id="link-69" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-69', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno"> 363</tt>  <tt class="py-line">                <tt class="py-keyword">yield</tt> <tt id="link-70" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-70', 'r', 'link-64');">r</a></tt> </tt>
</div><a name="L364"></a><tt class="py-lineno"> 364</tt>  <tt class="py-line"><tt class="py-comment">#                except:</tt> </tt>
<a name="L365"></a><tt class="py-lineno"> 365</tt>  <tt class="py-line"><tt class="py-comment">#                    print var.keys(),  var.values()</tt> </tt>
<a name="L366"></a><tt class="py-lineno"> 366</tt>  <tt class="py-line">                     </tt>
<a name="L367"></a><tt class="py-lineno"> 367</tt>  <tt class="py-line">        <tt class="py-name">create</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L368"></a><tt class="py-lineno"> 368</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">dbname</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'.sqlite'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L369"></a><tt class="py-lineno"> 369</tt>  <tt class="py-line">            <tt class="py-name">dbname</tt> <tt class="py-op">+=</tt> <tt class="py-string">'.sqlite'</tt> </tt>
<a name="L370"></a><tt class="py-lineno"> 370</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L371"></a><tt class="py-lineno"> 371</tt>  <tt class="py-line">            <tt class="py-name">create</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L372"></a><tt class="py-lineno"> 372</tt>  <tt class="py-line">        <tt class="py-name">con</tt> <tt class="py-op">=</tt> <tt class="py-name">sqlite3</tt><tt class="py-op">.</tt><tt class="py-name">connect</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno"> 373</tt>  <tt class="py-line">        <tt class="py-comment">#create tables</tt> </tt>
<a name="L374"></a><tt class="py-lineno"> 374</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L375"></a><tt class="py-lineno"> 375</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno"> 376</tt>  <tt class="py-line">                <tt class="py-name">labs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L377"></a><tt class="py-lineno"> 377</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">k2</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">v</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno"> 378</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">v2</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno"> 379</tt>  <tt class="py-line">                        <tt class="py-name">labs</tt><tt class="py-op">+=</tt><tt class="py-op">[</tt><tt class="py-name">k2</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">v2</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L380"></a><tt class="py-lineno"> 380</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L381"></a><tt class="py-lineno"> 381</tt>  <tt class="py-line">                        <tt class="py-name">labs</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">k2</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno"> 382</tt>  <tt class="py-line">                <tt class="py-name">nv</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">labs</tt><tt class="py-op">)</tt><tt class="py-comment">#+1 #variables plus primary key</tt> </tt>
<a name="L383"></a><tt class="py-lineno"> 383</tt>  <tt class="py-line">                <tt class="py-name">tstrc</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">+</tt><tt class="py-string">'(pk integer primary key asc autoincrement,'</tt><tt class="py-op">+</tt><tt class="py-string">','</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">labs</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">')'</tt> </tt>
<a name="L384"></a><tt class="py-lineno"> 384</tt>  <tt class="py-line">                <tt class="py-name">tstr</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">+</tt><tt class="py-string">'('</tt><tt class="py-op">+</tt><tt class="py-string">','</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">labs</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">')'</tt> </tt>
<a name="L385"></a><tt class="py-lineno"> 385</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">create</tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno"> 386</tt>  <tt class="py-line">                    <tt class="py-name">con</tt><tt class="py-op">.</tt><tt class="py-name">execute</tt><tt class="py-op">(</tt><tt class="py-string">'create table '</tt><tt class="py-op">+</tt><tt class="py-name">tstrc</tt><tt class="py-op">)</tt> </tt>
<a name="L387"></a><tt class="py-lineno"> 387</tt>  <tt class="py-line"><tt class="py-comment">#            elif isinstance(v, numpy.recarray):</tt> </tt>
<a name="L388"></a><tt class="py-lineno"> 388</tt>  <tt class="py-line"><tt class="py-comment">#                nv = len(v.dtype.names) +1 #variables plus primary key</tt> </tt>
<a name="L389"></a><tt class="py-lineno"> 389</tt>  <tt class="py-line"><tt class="py-comment">#                tstr = k+"("+','.join(v.dtype.names)+')'</tt> </tt>
<a name="L390"></a><tt class="py-lineno"> 390</tt>  <tt class="py-line"><tt class="py-comment">#                if create:</tt> </tt>
<a name="L391"></a><tt class="py-lineno"> 391</tt>  <tt class="py-line"><tt class="py-comment">#                    con.execute("create table "+ tstrc)</tt> </tt>
<a name="L392"></a><tt class="py-lineno"> 392</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno"> 393</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Non-valid data structure."</tt><tt class="py-op">)</tt> </tt>
<a name="L394"></a><tt class="py-lineno"> 394</tt>  <tt class="py-line">            <tt class="py-comment">#print "insert into "+tstr+" values("+",".join(['?']*nv)+")"</tt> </tt>
<a name="L395"></a><tt class="py-lineno"> 395</tt>  <tt class="py-line">            <tt class="py-name">con</tt><tt class="py-op">.</tt><tt class="py-name">executemany</tt><tt class="py-op">(</tt><tt class="py-string">"insert into "</tt><tt class="py-op">+</tt><tt class="py-name">tstr</tt><tt class="py-op">+</tt><tt class="py-string">" values("</tt><tt class="py-op">+</tt><tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'?'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">")"</tt><tt class="py-op">,</tt> <tt class="py-name">row_generator</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L396"></a><tt class="py-lineno"> 396</tt>  <tt class="py-line">        <tt class="py-name">con</tt><tt class="py-op">.</tt><tt class="py-name">commit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L397"></a><tt class="py-lineno"> 397</tt>  <tt class="py-line">        <tt class="py-name">con</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="FitModel.run"></a><div id="FitModel.run-def"><a name="L398"></a><tt class="py-lineno"> 398</tt> <a class="py-toggle" href="#" id="FitModel.run-toggle" onclick="return toggle('FitModel.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">method</tt><tt class="py-op">,</tt><tt class="py-param">likvar</tt><tt class="py-op">,</tt><tt class="py-param">pool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-param">adjinits</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt><tt class="py-param">ew</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">=</tt><tt class="py-string">'results'</tt><tt class="py-op">,</tt> <tt class="py-param">monitor</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">initheta</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.run-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.run-expanded"><a name="L399"></a><tt class="py-lineno"> 399</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L400"></a><tt class="py-lineno"> 400</tt>  <tt class="py-line"><tt class="py-docstring">        Fit the model against data</tt> </tt>
<a name="L401"></a><tt class="py-lineno"> 401</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L402"></a><tt class="py-lineno"> 402</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L403"></a><tt class="py-lineno"> 403</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: dictionary with variable names and observed series, as Key and value respectively.</tt> </tt>
<a name="L404"></a><tt class="py-lineno"> 404</tt>  <tt class="py-line"><tt class="py-docstring">            - `method`: Inference method: "ABC", "SIR", "MCMC" or "DREAM"</tt> </tt>
<a name="L405"></a><tt class="py-lineno"> 405</tt>  <tt class="py-line"><tt class="py-docstring">            - `likvar`: Variance of the likelihood function in the SIR and MCMC method</tt> </tt>
<a name="L406"></a><tt class="py-lineno"> 406</tt>  <tt class="py-line"><tt class="py-docstring">            - `pool`: Pool priors on model's outputs.</tt> </tt>
<a name="L407"></a><tt class="py-lineno"> 407</tt>  <tt class="py-line"><tt class="py-docstring">            - `adjinits`: whether to adjust inits to data</tt> </tt>
<a name="L408"></a><tt class="py-lineno"> 408</tt>  <tt class="py-line"><tt class="py-docstring">            - `ew`: Whether to use expanding windows instead of moving ones.</tt> </tt>
<a name="L409"></a><tt class="py-lineno"> 409</tt>  <tt class="py-line"><tt class="py-docstring">            - `dbname`: name of the sqlite3 database</tt> </tt>
<a name="L410"></a><tt class="py-lineno"> 410</tt>  <tt class="py-line"><tt class="py-docstring">            - `monitor`: Whether to monitor certains variables during the inference. If not False, should be a list of valid phi variable names.</tt> </tt>
<a name="L411"></a><tt class="py-lineno"> 411</tt>  <tt class="py-line"><tt class="py-docstring">            - `initheta`: starting position in parameter space for the sampling to start. (only used by MCMC and DREAM) </tt> </tt>
<a name="L412"></a><tt class="py-lineno"> 412</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L413"></a><tt class="py-lineno"> 413</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ew</tt> <tt class="py-op">=</tt> <tt class="py-name">ew</tt> </tt>
<a name="L414"></a><tt class="py-lineno"> 414</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adjinits</tt> <tt class="py-op">=</tt> <tt class="py-name">adjinits</tt> </tt>
<a name="L415"></a><tt class="py-lineno"> 415</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pool</tt> <tt class="py-op">=</tt> <tt class="py-name">pool</tt> </tt>
<a name="L416"></a><tt class="py-lineno"> 416</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">initheta</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt> <tt class="py-comment">#type checking</tt> </tt>
<a name="L417"></a><tt class="py-lineno"> 417</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">initheta</tt> <tt class="py-op">=</tt> <tt class="py-name">initheta</tt> </tt>
<a name="L418"></a><tt class="py-lineno"> 418</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prior_set</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> </tt>
<a name="L419"></a><tt class="py-lineno"> 419</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">monitor</tt><tt class="py-op">:</tt> </tt>
<a name="L420"></a><tt class="py-lineno"> 420</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._monitor_setup()=trunk.BIP.Bayes.Melding.FitModel-class.html#_monitor_setup"><a title="trunk.BIP.Bayes.Melding.FitModel._monitor_setup" class="py-name" href="#" onclick="return doclink('link-71', '_monitor_setup', 'link-71');">_monitor_setup</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L421"></a><tt class="py-lineno"> 421</tt>  <tt class="py-line">        <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno"> 422</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt> </tt>
<a name="L423"></a><tt class="py-lineno"> 423</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'theta'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'phi'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L424"></a><tt class="py-lineno"> 424</tt>  <tt class="py-line">        <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-string">'rm %s_*.pickle'</tt><tt class="py-op">%</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno"> 425</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno"> 426</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> <tt class="py-op">=</tt> <tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt> </tt>
<a name="L427"></a><tt class="py-lineno"> 427</tt>  <tt class="py-line">        <tt class="py-name">wl</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> </tt>
<a name="L428"></a><tt class="py-lineno"> 428</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L429"></a><tt class="py-lineno"> 429</tt>  <tt class="py-line">            <tt id="link-72" class="py-name" targets="Variable trunk.BIP.SDE.example.t0=trunk.BIP.SDE.example-module.html#t0"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-72', 't0', 'link-72');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L430"></a><tt class="py-lineno"> 430</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; Window # %s of %s!'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno"> 431</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">w</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno"> 432</tt>  <tt class="py-line">                <tt class="py-name">rt</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">-</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">tel</tt> </tt>
<a name="L433"></a><tt class="py-lineno"> 433</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Remaining time: %s minutes and %s seconds."</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">rt</tt><tt class="py-op">//</tt><tt class="py-number">60</tt><tt class="py-op">,</tt> <tt class="py-name">rt</tt><tt class="py-op">%</tt><tt class="py-number">60</tt><tt class="py-op">)</tt> </tt>
<a name="L434"></a><tt class="py-lineno"> 434</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt> <tt class="py-keyword">if</tt> <tt class="py-name">ew</tt> <tt class="py-keyword">else</tt> <tt class="py-name">wl</tt> <tt class="py-comment">#setting tf according to window type</tt> </tt>
<a name="L435"></a><tt class="py-lineno"> 435</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-73', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'tf'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt> </tt>
<a name="L436"></a><tt class="py-lineno"> 436</tt>  <tt class="py-line">            <tt class="py-name">d2</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L437"></a><tt class="py-lineno"> 437</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment">#Slicing data to the current window</tt> </tt>
<a name="L438"></a><tt class="py-lineno"> 438</tt>  <tt class="py-line">                <tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">v</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">ew</tt> <tt class="py-keyword">else</tt> <tt class="py-name">v</tt><tt class="py-op">[</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt><tt class="py-op">:</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt><tt class="py-op">+</tt><tt class="py-name">wl</tt><tt class="py-op">]</tt>             </tt>
<a name="L439"></a><tt class="py-lineno"> 439</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">w</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">adjinits</tt><tt class="py-op">:</tt> </tt>
<a name="L440"></a><tt class="py-lineno"> 440</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno"> 441</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno"> 442</tt>  <tt class="py-line">                        <tt class="py-keyword">continue</tt> </tt>
<a name="L443"></a><tt class="py-lineno"> 443</tt>  <tt class="py-line">                    <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L444"></a><tt class="py-lineno"> 444</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt>  <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt> <tt class="py-op">)</tt> <tt class="py-keyword">else</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">nanmean</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L445"></a><tt class="py-lineno"> 445</tt>  <tt class="py-line">                    <tt class="py-comment">#TODO: figure out how to balance the total pop</tt> </tt>
<a name="L446"></a><tt class="py-lineno"> 446</tt>  <tt class="py-line"><tt class="py-comment">#                    self.inits[0] += self.totpop-sum(self.inits) #adjusting susceptibles</tt> </tt>
<a name="L447"></a><tt class="py-lineno"> 447</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-74', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'inits'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> </tt>
<a name="L448"></a><tt class="py-lineno"> 448</tt>  <tt class="py-line">            <tt id="link-75" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-75', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt> <tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel.do_inference()=trunk.BIP.Bayes.Melding.FitModel-class.html#do_inference"><a title="trunk.BIP.Bayes.Melding.FitModel.do_inference" class="py-name" href="#" onclick="return doclink('link-76', 'do_inference', 'link-76');">do_inference</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">d2</tt><tt class="py-op">,</tt> <tt class="py-name">prior</tt><tt class="py-op">=</tt><tt class="py-name">prior</tt><tt class="py-op">,</tt><tt class="py-name">predlen</tt><tt class="py-op">=</tt><tt class="py-name">wl</tt><tt class="py-op">,</tt> <tt class="py-name">method</tt><tt class="py-op">=</tt><tt class="py-name">method</tt><tt class="py-op">,</tt><tt class="py-name">likvar</tt><tt class="py-op">=</tt><tt class="py-name">likvar</tt><tt class="py-op">)</tt> </tt>
<a name="L449"></a><tt class="py-lineno"> 449</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">stop_now</tt><tt class="py-op">:</tt> </tt>
<a name="L450"></a><tt class="py-lineno"> 450</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> </tt>
<a name="L451"></a><tt class="py-lineno"> 451</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt> <tt class="py-op">+=</tt> <tt class="py-number">2.</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">likmax</tt><tt class="py-op">)</tt> <tt class="py-comment"># 2k - 2 ln(L)</tt> </tt>
<a name="L452"></a><tt class="py-lineno"> 452</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt> <tt class="py-op">*</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">*</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">2.</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">likmax</tt> <tt class="py-comment"># k ln(n) - 2 ln(L)</tt> </tt>
<a name="L453"></a><tt class="py-lineno"> 453</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-77', 'DIC', 'link-30');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-78', 'DIC', 'link-30');">DIC</a></tt> </tt>
<a name="L454"></a><tt class="py-lineno"> 454</tt>  <tt class="py-line">            <tt class="py-comment"># ===Saving results===</tt> </tt>
<a name="L455"></a><tt class="py-lineno"> 455</tt>  <tt class="py-line">            <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'%s_%s%s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-string">".pickle"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L456"></a><tt class="py-lineno"> 456</tt>  <tt class="py-line">            <tt class="py-comment">#save weekly posteriors of theta and phi, posteriors of series, data (d) and predictions(z)</tt> </tt>
<a name="L457"></a><tt class="py-lineno"> 457</tt>  <tt class="py-line">            <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-79', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt> <tt class="py-name">att</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L458"></a><tt class="py-lineno"> 458</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L459"></a><tt class="py-lineno"> 459</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">dbname</tt><tt class="py-op">:</tt> </tt>
<a name="L460"></a><tt class="py-lineno"> 460</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">+</tt><tt class="py-string">".sqlite"</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">w</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L461"></a><tt class="py-lineno"> 461</tt>  <tt class="py-line">                    <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">remove</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">+</tt><tt class="py-string">".sqlite"</tt><tt class="py-op">)</tt> </tt>
<a name="L462"></a><tt class="py-lineno"> 462</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._format_db_tables()=trunk.BIP.Bayes.Melding.FitModel-class.html#_format_db_tables"><a title="trunk.BIP.Bayes.Melding.FitModel._format_db_tables" class="py-name" href="#" onclick="return doclink('link-80', '_format_db_tables', 'link-80');">_format_db_tables</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-81', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt> <tt class="py-name">series</tt><tt class="py-op">,</tt> <tt class="py-name">predseries</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-82', 'DIC', 'link-30');">DIC</a></tt><tt class="py-op">)</tt> </tt>
<a name="L463"></a><tt class="py-lineno"> 463</tt>  <tt class="py-line">            <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'theta'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'phi'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L464"></a><tt class="py-lineno"> 464</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-83" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-83', 'pt', 'link-52');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L465"></a><tt class="py-lineno"> 465</tt>  <tt class="py-line">                <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-84', 'pt', 'link-52');">pt</a></tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno"> 466</tt>  <tt class="py-line">            <tt class="py-comment">#beta,alpha,sigma,Ri  = median(pt.beta),median(pt.alpha),median(pt.sigma),median(pt.Ri</tt> </tt>
<a name="L467"></a><tt class="py-lineno"> 467</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno"> 468</tt>  <tt class="py-line">                <tt class="py-comment">#print compress(isinf(pp[n]),pp[n])</tt> </tt>
<a name="L469"></a><tt class="py-lineno"> 469</tt>  <tt class="py-line">                <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'phi'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno"> 470</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">monitor</tt><tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno"> 471</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._monitor_plot()=trunk.BIP.Bayes.Melding.FitModel-class.html#_monitor_plot"><a title="trunk.BIP.Bayes.Melding.FitModel._monitor_plot" class="py-name" href="#" onclick="return doclink('link-85', '_monitor_plot', 'link-85');">_monitor_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">prior</tt><tt class="py-op">,</tt><tt class="py-name">d2</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">vars</tt><tt class="py-op">=</tt><tt class="py-name">monitor</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno"> 472</tt>  <tt class="py-line">             </tt>
<a name="L473"></a><tt class="py-lineno"> 473</tt>  <tt class="py-line">            <tt class="py-name">tel</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-86" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-86', 't0', 'link-72');">t0</a></tt> </tt>
<a name="L474"></a><tt class="py-lineno"> 474</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt> <tt class="py-op">/=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt> <tt class="py-comment">#averaging</tt> </tt>
<a name="L475"></a><tt class="py-lineno"> 475</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt> <tt class="py-op">/=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt> </tt>
<a name="L476"></a><tt class="py-lineno"> 476</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt> </tt>
<a name="L477"></a><tt class="py-lineno"> 477</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt> </tt>
<a name="L478"></a><tt class="py-lineno"> 478</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-87', 'DIC', 'link-30');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-88', 'DIC', 'link-30');">DIC</a></tt> </tt>
<a name="L479"></a><tt class="py-lineno"> 479</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"time: %s seconds"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">start</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno"> 480</tt>  <tt class="py-line">         </tt>
<a name="L481"></a><tt class="py-lineno"> 481</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L482"></a><tt class="py-lineno"> 482</tt>  <tt class="py-line">     </tt>
<a name="FitModel._format_db_tables"></a><div id="FitModel._format_db_tables-def"><a name="L483"></a><tt class="py-lineno"> 483</tt> <a class="py-toggle" href="#" id="FitModel._format_db_tables-toggle" onclick="return toggle('FitModel._format_db_tables');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_format_db_tables">_format_db_tables</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">w</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">pt</tt><tt class="py-op">,</tt> <tt class="py-param">series</tt><tt class="py-op">,</tt> <tt class="py-param">predseries</tt><tt class="py-op">,</tt> <tt class="py-param">AIC</tt><tt class="py-op">,</tt> <tt class="py-param">BIC</tt><tt class="py-op">,</tt> <tt class="py-param">DIC</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._format_db_tables-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._format_db_tables-expanded"><a name="L484"></a><tt class="py-lineno"> 484</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L485"></a><tt class="py-lineno"> 485</tt>  <tt class="py-line"><tt class="py-docstring">        Formats results for writing to database</tt> </tt>
<a name="L486"></a><tt class="py-lineno"> 486</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L487"></a><tt class="py-lineno"> 487</tt>  <tt class="py-line">        <tt class="py-comment">#TODO: Write tests for this</tt> </tt>
<a name="L488"></a><tt class="py-lineno"> 488</tt>  <tt class="py-line">        <tt class="py-comment"># data table does not require formatting</tt> </tt>
<a name="L489"></a><tt class="py-lineno"> 489</tt>  <tt class="py-line">        <tt class="py-comment"># Dates for this window</tt> </tt>
<a name="L490"></a><tt class="py-lineno"> 490</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L491"></a><tt class="py-lineno"> 491</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">'time'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno"> 492</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'time'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L493"></a><tt class="py-lineno"> 493</tt>  <tt class="py-line">                <tt class="py-name">ts</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'time'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno"> 494</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L495"></a><tt class="py-lineno"> 495</tt>  <tt class="py-line">                <tt class="py-name">ts</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'time'</tt><tt class="py-op">]</tt> </tt>
<a name="L496"></a><tt class="py-lineno"> 496</tt>  <tt class="py-line">            <tt class="py-name">dates</tt> <tt class="py-op">=</tt> <tt class="py-name">ts</tt><tt class="py-op">[</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">:</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">]</tt> </tt>
<a name="L497"></a><tt class="py-lineno"> 497</tt>  <tt class="py-line">            <tt class="py-name">preddates</tt> <tt class="py-op">=</tt> <tt class="py-name">ts</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">]</tt> </tt>
<a name="L498"></a><tt class="py-lineno"> 498</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L499"></a><tt class="py-lineno"> 499</tt>  <tt class="py-line">            <tt class="py-name">dates</tt> <tt class="py-op">=</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L500"></a><tt class="py-lineno"> 500</tt>  <tt class="py-line">            <tt class="py-name">preddates</tt> <tt class="py-op">=</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno"> 501</tt>  <tt class="py-line">        <tt class="py-comment"># Parameters table</tt> </tt>
<a name="L502"></a><tt class="py-lineno"> 502</tt>  <tt class="py-line">        <tt class="py-name">ptd</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'time'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-name">dates</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-89', 'pt', 'link-52');">pt</a></tt><tt class="py-op">[</tt><tt id="link-90" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-90', 'pt', 'link-52');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">}</tt> </tt>
<a name="L503"></a><tt class="py-lineno"> 503</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-91" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-91', 'pt', 'link-52');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L504"></a><tt class="py-lineno"> 504</tt>  <tt class="py-line">            <tt class="py-name">ptd</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-92', 'pt', 'link-52');">pt</a></tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L505"></a><tt class="py-lineno"> 505</tt>  <tt class="py-line">        <tt class="py-comment"># Series table</tt> </tt>
<a name="L506"></a><tt class="py-lineno"> 506</tt>  <tt class="py-line">        <tt class="py-name">seriesd</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'time'</tt><tt class="py-op">:</tt><tt class="py-name">dates</tt><tt class="py-op">*</tt><tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L507"></a><tt class="py-lineno"> 507</tt>  <tt class="py-line">        <tt class="py-name">predseriesd</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'time'</tt><tt class="py-op">:</tt><tt class="py-name">preddates</tt><tt class="py-op">*</tt><tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L508"></a><tt class="py-lineno"> 508</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L509"></a><tt class="py-lineno"> 509</tt>  <tt class="py-line">            <tt class="py-name">seriesd</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L510"></a><tt class="py-lineno"> 510</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">predseries</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L511"></a><tt class="py-lineno"> 511</tt>  <tt class="py-line">            <tt class="py-name">predseriesd</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">predseries</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L512"></a><tt class="py-lineno"> 512</tt>  <tt class="py-line">        <tt class="py-comment"># AIC and BIC table</tt> </tt>
<a name="L513"></a><tt class="py-lineno"> 513</tt>  <tt class="py-line">        <tt class="py-name">gof</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'time'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-name">dates</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'AIC'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-name">AIC</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'BIC'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-name">BIC</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'DIC'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt id="link-93" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-93', 'DIC', 'link-30');">DIC</a></tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L514"></a><tt class="py-lineno"> 514</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._save_to_db()=trunk.BIP.Bayes.Melding.FitModel-class.html#_save_to_db"><a title="trunk.BIP.Bayes.Melding.FitModel._save_to_db" class="py-name" href="#" onclick="return doclink('link-94', '_save_to_db', 'link-94');">_save_to_db</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">'post_theta'</tt><tt class="py-op">:</tt><tt class="py-name">ptd</tt><tt class="py-op">,</tt>  </tt>
<a name="L515"></a><tt class="py-lineno"> 515</tt>  <tt class="py-line">                                                                     <tt class="py-string">'series'</tt><tt class="py-op">:</tt><tt class="py-name">seriesd</tt><tt class="py-op">,</tt>  </tt>
<a name="L516"></a><tt class="py-lineno"> 516</tt>  <tt class="py-line">                                                                     <tt class="py-string">'data'</tt><tt class="py-op">:</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt>  </tt>
<a name="L517"></a><tt class="py-lineno"> 517</tt>  <tt class="py-line">                                                                     <tt class="py-string">'predicted_series'</tt><tt class="py-op">:</tt><tt class="py-name">predseriesd</tt><tt class="py-op">,</tt>  </tt>
<a name="L518"></a><tt class="py-lineno"> 518</tt>  <tt class="py-line">                                                                     <tt class="py-string">'GOF'</tt><tt class="py-op">:</tt><tt class="py-name">gof</tt><tt class="py-op">,</tt> </tt>
<a name="L519"></a><tt class="py-lineno"> 519</tt>  <tt class="py-line">                                                                     <tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
</div><a name="L520"></a><tt class="py-lineno"> 520</tt>  <tt class="py-line">     </tt>
<a name="FitModel._monitor_setup"></a><div id="FitModel._monitor_setup-def"><a name="L521"></a><tt class="py-lineno"> 521</tt> <a class="py-toggle" href="#" id="FitModel._monitor_setup-toggle" onclick="return toggle('FitModel._monitor_setup');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_monitor_setup">_monitor_setup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._monitor_setup-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._monitor_setup-expanded"><a name="L522"></a><tt class="py-lineno"> 522</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L523"></a><tt class="py-lineno"> 523</tt>  <tt class="py-line"><tt class="py-docstring">        Sets up realtime plotting for inference</tt> </tt>
<a name="L524"></a><tt class="py-lineno"> 524</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L525"></a><tt class="py-lineno"> 525</tt>  <tt class="py-line">        <tt class="py-comment">#theta histograms (for current window)</tt> </tt>
<a name="L526"></a><tt class="py-lineno"> 526</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hst</tt> <tt class="py-op">=</tt> <tt class="py-name">xmlrpclib</tt><tt class="py-op">.</tt><tt class="py-name">ServerProxy</tt><tt class="py-op">(</tt><tt class="py-string">'http://localhost:%s'</tt><tt class="py-op">%</tt><tt id="link-95" class="py-name"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-95', 'rpc_plot', 'link-12');">rpc_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">hold</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">allow_none</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-comment">#RTplot() </tt> </tt>
<a name="L527"></a><tt class="py-lineno"> 527</tt>  <tt class="py-line">        <tt class="py-comment">#full data and simulated series</tt> </tt>
<a name="L528"></a><tt class="py-lineno"> 528</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fsp</tt> <tt class="py-op">=</tt> <tt class="py-name">xmlrpclib</tt><tt class="py-op">.</tt><tt class="py-name">ServerProxy</tt><tt class="py-op">(</tt><tt class="py-string">'http://localhost:%s'</tt><tt class="py-op">%</tt><tt id="link-96" class="py-name"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-96', 'rpc_plot', 'link-12');">rpc_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">hold</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">allow_none</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-comment">#RTplot()</tt> </tt>
<a name="L529"></a><tt class="py-lineno"> 529</tt>  <tt class="py-line">        <tt class="py-comment"># phi time series (model output for the current window)</tt> </tt>
<a name="L530"></a><tt class="py-lineno"> 530</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ser</tt> <tt class="py-op">=</tt> <tt class="py-name">xmlrpclib</tt><tt class="py-op">.</tt><tt class="py-name">ServerProxy</tt><tt class="py-op">(</tt><tt class="py-string">'http://localhost:%s'</tt><tt class="py-op">%</tt><tt id="link-97" class="py-name"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-97', 'rpc_plot', 'link-12');">rpc_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">hold</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">allow_none</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-comment">#RTplot()</tt> </tt>
</div><a name="L531"></a><tt class="py-lineno"> 531</tt>  <tt class="py-line"> </tt>
<a name="FitModel._get95_bands"></a><div id="FitModel._get95_bands-def"><a name="L532"></a><tt class="py-lineno"> 532</tt> <a class="py-toggle" href="#" id="FitModel._get95_bands-toggle" onclick="return toggle('FitModel._get95_bands');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_get95_bands">_get95_bands</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">vname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._get95_bands-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._get95_bands-expanded"><a name="L533"></a><tt class="py-lineno"> 533</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L534"></a><tt class="py-lineno"> 534</tt>  <tt class="py-line"><tt class="py-docstring">        Returns 95% bands for series of all variables in vname</tt> </tt>
<a name="L535"></a><tt class="py-lineno"> 535</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L536"></a><tt class="py-lineno"> 536</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L537"></a><tt class="py-lineno"> 537</tt>  <tt class="py-line"><tt class="py-docstring">            - `series`: record array containing the series</tt> </tt>
<a name="L538"></a><tt class="py-lineno"> 538</tt>  <tt class="py-line"><tt class="py-docstring">            - `vname`: list of strings of variables in series for which we want to get the bands</tt> </tt>
<a name="L539"></a><tt class="py-lineno"> 539</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L540"></a><tt class="py-lineno"> 540</tt>  <tt class="py-line">        <tt class="py-name">i5</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">2.5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">vname</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno"> 541</tt>  <tt class="py-line">        <tt class="py-name">i95</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">97.5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">vname</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno"> 542</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">i5</tt><tt class="py-op">,</tt><tt class="py-name">i95</tt> </tt>
</div><a name="L543"></a><tt class="py-lineno"> 543</tt>  <tt class="py-line">         </tt>
<a name="FitModel._long_term_prediction_plot"></a><div id="FitModel._long_term_prediction_plot-def"><a name="L544"></a><tt class="py-lineno"> 544</tt> <a class="py-toggle" href="#" id="FitModel._long_term_prediction_plot-toggle" onclick="return toggle('FitModel._long_term_prediction_plot');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_long_term_prediction_plot">_long_term_prediction_plot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cpars</tt><tt class="py-op">,</tt><tt class="py-param">vind</tt><tt class="py-op">,</tt>  <tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._long_term_prediction_plot-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._long_term_prediction_plot-expanded"><a name="L545"></a><tt class="py-lineno"> 545</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L546"></a><tt class="py-lineno"> 546</tt>  <tt class="py-line"><tt class="py-docstring">        Plots the simulated trajectory predicted from best fit parameters.</tt> </tt>
<a name="L547"></a><tt class="py-lineno"> 547</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L548"></a><tt class="py-lineno"> 548</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L549"></a><tt class="py-lineno"> 549</tt>  <tt class="py-line"><tt class="py-docstring">            - `cpars`: best fit  parameter set</tt> </tt>
<a name="L550"></a><tt class="py-lineno"> 550</tt>  <tt class="py-line"><tt class="py-docstring">            - `vind`: List with indices(in self.phinames) to variables to be plotted </tt> </tt>
<a name="L551"></a><tt class="py-lineno"> 551</tt>  <tt class="py-line"><tt class="py-docstring">            - `w`: current window number.</tt> </tt>
<a name="L552"></a><tt class="py-lineno"> 552</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L553"></a><tt class="py-lineno"> 553</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">full_len</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L554"></a><tt class="py-lineno"> 554</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L555"></a><tt class="py-lineno"> 555</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-98', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'tf'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">full_len</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ew</tt> <tt class="py-keyword">else</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">full_len</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L556"></a><tt class="py-lineno"> 556</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ew</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-99', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'inits'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">finits</tt> </tt>
<a name="L557"></a><tt class="py-lineno"> 557</tt>  <tt class="py-line">        <tt class="py-name">simseries</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-100', 'model', 'link-22');">model</a></tt><tt class="py-op">(</tt><tt class="py-name">cpars</tt><tt class="py-op">)</tt> </tt>
<a name="L558"></a><tt class="py-lineno"> 558</tt>  <tt class="py-line">        <tt class="py-name">simseries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">simseries</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">vind</tt><tt class="py-op">]</tt> </tt>
<a name="L559"></a><tt class="py-lineno"> 559</tt>  <tt class="py-line">        <tt class="py-name">snames</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">n</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">vind</tt><tt class="py-op">]</tt> </tt>
<a name="L560"></a><tt class="py-lineno"> 560</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-101', 'model', 'link-22');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">func_globals</tt><tt class="py-op">[</tt><tt class="py-string">'tf'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt> </tt>
<a name="L561"></a><tt class="py-lineno"> 561</tt>  <tt class="py-line">        <tt class="py-name">xinit</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ew</tt> <tt class="py-keyword">else</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">*</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> </tt>
<a name="L562"></a><tt class="py-lineno"> 562</tt>  <tt class="py-line"><tt class="py-comment">#        print xinit, xinit+len(simseries[0])</tt> </tt>
<a name="L563"></a><tt class="py-lineno"> 563</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fsp</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">simseries</tt><tt class="py-op">,</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">xinit</tt><tt class="py-op">,</tt><tt class="py-name">xinit</tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">simseries</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">snames</tt><tt class="py-op">,</tt> <tt class="py-string">"Best fit simulation after window %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L564"></a><tt class="py-lineno"> 564</tt>  <tt class="py-line">     </tt>
<a name="L565"></a><tt class="py-lineno"> 565</tt>  <tt class="py-line">         </tt>
<a name="L566"></a><tt class="py-lineno"> 566</tt>  <tt class="py-line">     </tt>
<a name="FitModel._monitor_plot"></a><div id="FitModel._monitor_plot-def"><a name="L567"></a><tt class="py-lineno"> 567</tt> <a class="py-toggle" href="#" id="FitModel._monitor_plot-toggle" onclick="return toggle('FitModel._monitor_plot');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_monitor_plot">_monitor_plot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">series</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">,</tt> <tt class="py-param">d2</tt><tt class="py-op">,</tt><tt class="py-param">w</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">vars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._monitor_plot-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._monitor_plot-expanded"><a name="L568"></a><tt class="py-lineno"> 568</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L569"></a><tt class="py-lineno"> 569</tt>  <tt class="py-line"><tt class="py-docstring">        Plots real time data</tt> </tt>
<a name="L570"></a><tt class="py-lineno"> 570</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L571"></a><tt class="py-lineno"> 571</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L572"></a><tt class="py-lineno"> 572</tt>  <tt class="py-line"><tt class="py-docstring">            - `series`: Record array with the simulated series.</tt> </tt>
<a name="L573"></a><tt class="py-lineno"> 573</tt>  <tt class="py-line"><tt class="py-docstring">            - `prior`: Dctionary with the prior sample of Theta</tt> </tt>
<a name="L574"></a><tt class="py-lineno"> 574</tt>  <tt class="py-line"><tt class="py-docstring">            - `d2`: Dictionary with data for the current fitting window.</tt> </tt>
<a name="L575"></a><tt class="py-lineno"> 575</tt>  <tt class="py-line"><tt class="py-docstring">            - `w`: Integer id of the current fitting window.</tt> </tt>
<a name="L576"></a><tt class="py-lineno"> 576</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Dictionary with the full dataset.</tt> </tt>
<a name="L577"></a><tt class="py-lineno"> 577</tt>  <tt class="py-line"><tt class="py-docstring">            - `vars`: List with variable names to be plotted.</tt> </tt>
<a name="L578"></a><tt class="py-lineno"> 578</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L579"></a><tt class="py-lineno"> 579</tt>  <tt class="py-line"><tt class="py-comment">#        diff = 0</tt> </tt>
<a name="L580"></a><tt class="py-lineno"> 580</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">vn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L581"></a><tt class="py-lineno"> 581</tt>  <tt class="py-line">            <tt class="py-comment">#sum errors for all oserved variables</tt> </tt>
<a name="L582"></a><tt class="py-lineno"> 582</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L583"></a><tt class="py-lineno"> 583</tt>  <tt class="py-line">                <tt class="py-name">diff</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">nanmean</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L584"></a><tt class="py-lineno"> 584</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L585"></a><tt class="py-lineno"> 585</tt>  <tt class="py-line">                <tt class="py-name">diff</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">vn</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L586"></a><tt class="py-lineno"> 586</tt>  <tt class="py-line"><tt class="py-comment">#        print diff, min(diff)</tt> </tt>
<a name="L587"></a><tt class="py-lineno"> 587</tt>  <tt class="py-line">        <tt class="py-name">initind</tt> <tt class="py-op">=</tt> <tt class="py-name">diff</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">diff</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L588"></a><tt class="py-lineno"> 588</tt>  <tt class="py-line">        <tt class="py-name">vindices</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">vars</tt><tt class="py-op">]</tt> </tt>
<a name="L589"></a><tt class="py-lineno"> 589</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">vars</tt><tt class="py-op">:</tt> </tt>
<a name="L590"></a><tt class="py-lineno"> 590</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d2</tt><tt class="py-op">:</tt> </tt>
<a name="L591"></a><tt class="py-lineno"> 591</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L592"></a><tt class="py-lineno"> 592</tt>  <tt class="py-line">            <tt class="py-name">i5</tt><tt class="py-op">,</tt><tt class="py-name">i95</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._get95_bands()=trunk.BIP.Bayes.Melding.FitModel-class.html#_get95_bands"><a title="trunk.BIP.Bayes.Melding.FitModel._get95_bands" class="py-name" href="#" onclick="return doclink('link-102', '_get95_bands', 'link-102');">_get95_bands</a></tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L593"></a><tt class="py-lineno"> 593</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ser</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">initind</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt>  <tt class="py-op">[</tt><tt class="py-string">"Best run's %s"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'Window %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L594"></a><tt class="py-lineno"> 594</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ser</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">i5</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">'2.5%'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'Window %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L595"></a><tt class="py-lineno"> 595</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ser</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">i95</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  <tt class="py-op">[</tt><tt class="py-string">'97.5%'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'Window %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L596"></a><tt class="py-lineno"> 596</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ser</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">'Obs. %s'</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'Window %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'points'</tt><tt class="py-op">)</tt> </tt>
<a name="L597"></a><tt class="py-lineno"> 597</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fsp</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">'Obs. %s'</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'Window %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'points'</tt><tt class="py-op">)</tt> </tt>
<a name="L598"></a><tt class="py-lineno"> 598</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hst</tt><tt class="py-op">.</tt><tt class="py-name">histogram</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">,</tt><tt class="py-string">'Window %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno"> 599</tt>  <tt class="py-line">        <tt class="py-name">cpars</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">initind</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L600"></a><tt class="py-lineno"> 600</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._long_term_prediction_plot()=trunk.BIP.Bayes.Melding.FitModel-class.html#_long_term_prediction_plot"><a title="trunk.BIP.Bayes.Melding.FitModel._long_term_prediction_plot" class="py-name" href="#" onclick="return doclink('link-103', '_long_term_prediction_plot', 'link-103');">_long_term_prediction_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">cpars</tt><tt class="py-op">,</tt><tt class="py-name">vindices</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L601"></a><tt class="py-lineno"> 601</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ser</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name" targets="Method trunk.BIP.Viz.realtime.RTplot.clearFig()=trunk.BIP.Viz.realtime.RTplot-class.html#clearFig"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-104', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L602"></a><tt class="py-lineno"> 602</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hst</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-105', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L603"></a><tt class="py-lineno"> 603</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fsp</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-106', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L604"></a><tt class="py-lineno"> 604</tt>  <tt class="py-line">     </tt>
<a name="FitModel.plot_results"></a><div id="FitModel.plot_results-def"><a name="L605"></a><tt class="py-lineno"> 605</tt> <a class="py-toggle" href="#" id="FitModel.plot_results-toggle" onclick="return toggle('FitModel.plot_results');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#plot_results">plot_results</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  <tt class="py-param">dbname</tt><tt class="py-op">=</tt><tt class="py-string">"results"</tt><tt class="py-op">,</tt> <tt class="py-param">savefigs</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.plot_results-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel.plot_results-expanded"><a name="L606"></a><tt class="py-lineno"> 606</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L607"></a><tt class="py-lineno"> 607</tt>  <tt class="py-line"><tt class="py-docstring">        Plot the final results of the inference</tt> </tt>
<a name="L608"></a><tt class="py-lineno"> 608</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L609"></a><tt class="py-lineno"> 609</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L610"></a><tt class="py-lineno"> 610</tt>  <tt class="py-line">            <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt> </tt>
<a name="L611"></a><tt class="py-lineno"> 611</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> <tt class="py-comment">#read the data files</tt> </tt>
<a name="L612"></a><tt class="py-lineno"> 612</tt>  <tt class="py-line">            <tt id="link-107" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-107', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel._read_results()=trunk.BIP.Bayes.Melding.FitModel-class.html#_read_results"><a title="trunk.BIP.Bayes.Melding.FitModel._read_results" class="py-name" href="#" onclick="return doclink('link-108', '_read_results', 'link-108');">_read_results</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno"> 613</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L614"></a><tt class="py-lineno"> 614</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt><tt class="py-op">:</tt> </tt>
<a name="L615"></a><tt class="py-lineno"> 615</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> </tt>
<a name="L616"></a><tt class="py-lineno"> 616</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">has_key</tt><tt class="py-op">(</tt><tt class="py-string">'time'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L617"></a><tt class="py-lineno"> 617</tt>  <tt class="py-line">            <tt class="py-name">tim</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-string">'time'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L618"></a><tt class="py-lineno"> 618</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L619"></a><tt class="py-lineno"> 619</tt>  <tt class="py-line">            <tt class="py-name">tim</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L620"></a><tt class="py-lineno"> 620</tt>  <tt class="py-line">        <tt class="py-comment">#PM.plot_par_series(range(len(pt)),pt)</tt> </tt>
<a name="L621"></a><tt class="py-lineno"> 621</tt>  <tt class="py-line">        <tt class="py-name">priors</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel.prior_sample()=trunk.BIP.Bayes.Melding.FitModel-class.html#prior_sample"><a title="trunk.BIP.Bayes.Melding.FitModel.prior_sample" class="py-name" href="#" onclick="return doclink('link-109', 'prior_sample', 'link-109');">prior_sample</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L622"></a><tt class="py-lineno"> 622</tt>  <tt class="py-line">        <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Function trunk.BIP.Bayes.PlotMeld.plot_par_violin()=trunk.BIP.Bayes.PlotMeld-module.html#plot_par_violin"><a title="trunk.BIP.Bayes.PlotMeld.plot_par_violin" class="py-name" href="#" onclick="return doclink('link-110', 'plot_par_violin', 'link-110');">plot_par_violin</a></tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt id="link-111" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-111', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt> <tt class="py-name">priors</tt><tt class="py-op">)</tt> </tt>
<a name="L623"></a><tt class="py-lineno"> 623</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'windows'</tt><tt class="py-op">)</tt> </tt>
<a name="L624"></a><tt class="py-lineno"> 624</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savefigs</tt><tt class="py-op">:</tt> </tt>
<a name="L625"></a><tt class="py-lineno"> 625</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">+</tt><tt class="py-string">"_violin.svg"</tt><tt class="py-op">)</tt> </tt>
<a name="L626"></a><tt class="py-lineno"> 626</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L627"></a><tt class="py-lineno"> 627</tt>  <tt class="py-line">        <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Function trunk.BIP.Bayes.PlotMeld.plot_series2()=trunk.BIP.Bayes.PlotMeld-module.html#plot_series2"><a title="trunk.BIP.Bayes.PlotMeld.plot_series2" class="py-name" href="#" onclick="return doclink('link-112', 'plot_series2', 'link-112');">plot_series2</a></tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">names</tt><tt class="py-op">,</tt> <tt class="py-name">wl</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L628"></a><tt class="py-lineno"> 628</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savefigs</tt><tt class="py-op">:</tt> </tt>
<a name="L629"></a><tt class="py-lineno"> 629</tt>  <tt class="py-line">                <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">+</tt><tt class="py-string">"_series.svg"</tt><tt class="py-op">)</tt> </tt>
<a name="L630"></a><tt class="py-lineno"> 630</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L631"></a><tt class="py-lineno"> 631</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L632"></a><tt class="py-lineno"> 632</tt>  <tt class="py-line">            <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name" targets="Function trunk.BIP.Bayes.PlotMeld.pred_new_cases()=trunk.BIP.Bayes.PlotMeld-module.html#pred_new_cases"><a title="trunk.BIP.Bayes.PlotMeld.pred_new_cases" class="py-name" href="#" onclick="return doclink('link-113', 'pred_new_cases', 'link-113');">pred_new_cases</a></tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L633"></a><tt class="py-lineno"> 633</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">gca</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L634"></a><tt class="py-lineno"> 634</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'windows'</tt><tt class="py-op">)</tt> </tt>
<a name="L635"></a><tt class="py-lineno"> 635</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L636"></a><tt class="py-lineno"> 636</tt>  <tt class="py-line">            <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="trunk.BIP.Bayes.PlotMeld.plot_series2" class="py-name" href="#" onclick="return doclink('link-114', 'plot_series2', 'link-112');">plot_series2</a></tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">names</tt><tt class="py-op">,</tt> </tt>
<a name="L637"></a><tt class="py-lineno"> 637</tt>  <tt class="py-line">                            <tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Predicted vs. Observed series'</tt><tt class="py-op">,</tt><tt class="py-name">lag</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L638"></a><tt class="py-lineno"> 638</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'windows'</tt><tt class="py-op">)</tt> </tt>
<a name="L639"></a><tt class="py-lineno"> 639</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">savefigs</tt><tt class="py-op">:</tt> </tt>
<a name="L640"></a><tt class="py-lineno"> 640</tt>  <tt class="py-line">                <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">+</tt><tt class="py-string">"_predseries.svg"</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno"> 641</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L642"></a><tt class="py-lineno"> 642</tt>  <tt class="py-line"> </tt>
<a name="FitModel._read_results"></a><div id="FitModel._read_results-def"><a name="L643"></a><tt class="py-lineno"> 643</tt> <a class="py-toggle" href="#" id="FitModel._read_results-toggle" onclick="return toggle('FitModel._read_results');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.FitModel-class.html#_read_results">_read_results</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">nam</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._read_results-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="FitModel._read_results-expanded"><a name="L644"></a><tt class="py-lineno"> 644</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L645"></a><tt class="py-lineno"> 645</tt>  <tt class="py-line"><tt class="py-docstring">        read results from disk</tt> </tt>
<a name="L646"></a><tt class="py-lineno"> 646</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L647"></a><tt class="py-lineno"> 647</tt>  <tt class="py-line">        <tt id="link-115" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-115', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L648"></a><tt class="py-lineno"> 648</tt>  <tt class="py-line"> </tt>
<a name="L649"></a><tt class="py-lineno"> 649</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L650"></a><tt class="py-lineno"> 650</tt>  <tt class="py-line">            <tt class="py-name">fn</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s_%s.pickle"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">nam</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L651"></a><tt class="py-lineno"> 651</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-name">fn</tt> </tt>
<a name="L652"></a><tt class="py-lineno"> 652</tt>  <tt class="py-line">            <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fn</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L653"></a><tt class="py-lineno"> 653</tt>  <tt class="py-line">            <tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">pred</tt><tt class="py-op">,</tt> <tt class="py-name">samples</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L654"></a><tt class="py-lineno"> 654</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L655"></a><tt class="py-lineno"> 655</tt>  <tt class="py-line">            <tt id="link-116" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-116', 'pt', 'link-52');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L656"></a><tt class="py-lineno"> 656</tt>  <tt class="py-line">            <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> </tt>
<a name="L657"></a><tt class="py-lineno"> 657</tt>  <tt class="py-line">            <tt class="py-name">predseries</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pred</tt><tt class="py-op">)</tt> </tt>
<a name="L658"></a><tt class="py-lineno"> 658</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-117" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-117', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt> </tt>
</div></div><a name="L659"></a><tt class="py-lineno"> 659</tt>  <tt class="py-line">             </tt>
<a name="L660"></a><tt class="py-lineno"> 660</tt>  <tt class="py-line"> </tt>
<a name="Meld"></a><div id="Meld-def"><a name="L661"></a><tt class="py-lineno"> 661</tt> <a class="py-toggle" href="#" id="Meld-toggle" onclick="return toggle('Meld');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html">Meld</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="Meld-expanded"><a name="L662"></a><tt class="py-lineno"> 662</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L663"></a><tt class="py-lineno"> 663</tt>  <tt class="py-line"><tt class="py-docstring">    Bayesian Melding class</tt> </tt>
<a name="L664"></a><tt class="py-lineno"> 664</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Meld.__init__"></a><div id="Meld.__init__-def"><a name="L665"></a><tt class="py-lineno"> 665</tt> <a class="py-toggle" href="#" id="Meld.__init__-toggle" onclick="return toggle('Meld.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt>  <tt class="py-param">K</tt><tt class="py-op">,</tt>  <tt class="py-param">L</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">ntheta</tt><tt class="py-op">,</tt> <tt class="py-param">nphi</tt><tt class="py-op">,</tt> <tt class="py-param">alpha</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-param">verbose</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">viz</tt><tt class="py-op">=</tt><tt class="py-name">False</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.__init__-expanded"><a name="L666"></a><tt class="py-lineno"> 666</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L667"></a><tt class="py-lineno"> 667</tt>  <tt class="py-line"><tt class="py-docstring">        Initializes the Melding class.</tt> </tt>
<a name="L668"></a><tt class="py-lineno"> 668</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L669"></a><tt class="py-lineno"> 669</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L670"></a><tt class="py-lineno"> 670</tt>  <tt class="py-line"><tt class="py-docstring">            - `K`: Number of replicates of the model run. Also determines the prior sample size.</tt> </tt>
<a name="L671"></a><tt class="py-lineno"> 671</tt>  <tt class="py-line"><tt class="py-docstring">            - `L`: Number of samples from the Posterior distributions. Usually 10% of K.</tt> </tt>
<a name="L672"></a><tt class="py-lineno"> 672</tt>  <tt class="py-line"><tt class="py-docstring">            - `model`: Callable taking theta as argument and returning phi = M(theta).</tt> </tt>
<a name="L673"></a><tt class="py-lineno"> 673</tt>  <tt class="py-line"><tt class="py-docstring">            - `ntheta`: Number of inputs to the model (parameters).</tt> </tt>
<a name="L674"></a><tt class="py-lineno"> 674</tt>  <tt class="py-line"><tt class="py-docstring">            - `nphi`: Number of outputs of the model (State-variables)</tt> </tt>
<a name="L675"></a><tt class="py-lineno"> 675</tt>  <tt class="py-line"><tt class="py-docstring">            - `verbose`: 0,1, 2: whether to show more information about the computations</tt> </tt>
<a name="L676"></a><tt class="py-lineno"> 676</tt>  <tt class="py-line"><tt class="py-docstring">            - `viz`: Boolean. Wether to show graphical outputs of the fitting process</tt> </tt>
<a name="L677"></a><tt class="py-lineno"> 677</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L678"></a><tt class="py-lineno"> 678</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt> <tt class="py-op">=</tt> <tt class="py-name">K</tt> </tt>
<a name="L679"></a><tt class="py-lineno"> 679</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt> <tt class="py-op">=</tt> <tt class="py-name">L</tt> </tt>
<a name="L680"></a><tt class="py-lineno"> 680</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">=</tt> <tt class="py-name">verbose</tt> </tt>
<a name="L681"></a><tt class="py-lineno"> 681</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-118', 'model', 'link-22');">model</a></tt> <tt class="py-op">=</tt> <tt id="link-119" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-119', 'model', 'link-22');">model</a></tt> </tt>
<a name="L682"></a><tt class="py-lineno"> 682</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likelist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment">#list of likelihoods</tt> </tt>
<a name="L683"></a><tt class="py-lineno"> 683</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt> <tt class="py-comment">#Theta Priors (record array)</tt> </tt>
<a name="L684"></a><tt class="py-lineno"> 684</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt> <tt class="py-comment">#Theta Posteriors (record array)</tt> </tt>
<a name="L685"></a><tt class="py-lineno"> 685</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-comment">#Phi Priors (record array)</tt> </tt>
<a name="L686"></a><tt class="py-lineno"> 686</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-comment">#Phi model-induced Priors (record array)</tt> </tt>
<a name="L687"></a><tt class="py-lineno"> 687</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2type</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment">#list of distribution types</tt> </tt>
<a name="L688"></a><tt class="py-lineno"> 688</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-comment">#Phi Posteriors (record array)</tt> </tt>
<a name="L689"></a><tt class="py-lineno"> 689</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt> <tt class="py-op">=</tt> <tt class="py-name">ntheta</tt> </tt>
<a name="L690"></a><tt class="py-lineno"> 690</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nphi</tt> </tt>
<a name="L691"></a><tt class="py-lineno"> 691</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetapars</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L692"></a><tt class="py-lineno"> 692</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phipars</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L693"></a><tt class="py-lineno"> 693</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-name">alpha</tt> <tt class="py-comment">#pooling weight of user-provided phi priors</tt> </tt>
<a name="L694"></a><tt class="py-lineno"> 694</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L695"></a><tt class="py-lineno"> 695</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-comment">#parameterized rngs for each parameter</tt> </tt>
<a name="L696"></a><tt class="py-lineno"> 696</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi_dists</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-comment">#parameterized rngs for each variable</tt> </tt>
<a name="L697"></a><tt class="py-lineno"> 697</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likmax</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> </tt>
<a name="L698"></a><tt class="py-lineno"> 698</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">initheta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L699"></a><tt class="py-lineno"> 699</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AIC</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L700"></a><tt class="py-lineno"> 700</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">BIC</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L701"></a><tt class="py-lineno"> 701</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-120', 'DIC', 'link-30');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L702"></a><tt class="py-lineno"> 702</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stop_now</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> <tt class="py-comment">#Flag to interrupt fitting loop. inner loop checks this flag and exit when it is true.</tt> </tt>
<a name="L703"></a><tt class="py-lineno"> 703</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_step</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L704"></a><tt class="py-lineno"> 704</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">proposal_variance</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0000001</tt> </tt>
<a name="L705"></a><tt class="py-lineno"> 705</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-comment">#adaptive variance. Used my metropolis hastings</tt> </tt>
<a name="L706"></a><tt class="py-lineno"> 706</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">=</tt> <tt class="py-number">0.1</tt> <tt class="py-comment">#relaxation factor of the prior limits</tt> </tt>
<a name="L707"></a><tt class="py-lineno"> 707</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-121" class="py-name"><a title="trunk.BIP.Bayes.Melding.Viz
trunk.BIP.Viz" class="py-name" href="#" onclick="return doclink('link-121', 'Viz', 'link-9');">Viz</a></tt><tt class="py-op">:</tt> <tt class="py-comment">#Gnuplot installed</tt> </tt>
<a name="L708"></a><tt class="py-lineno"> 708</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name" targets="Variable trunk.BIP.SDE.gillespie.viz=trunk.BIP.SDE.gillespie-module.html#viz"><a title="trunk.BIP.SDE.gillespie.viz" class="py-name" href="#" onclick="return doclink('link-122', 'viz', 'link-122');">viz</a></tt> <tt class="py-op">=</tt> <tt id="link-123" class="py-name"><a title="trunk.BIP.SDE.gillespie.viz" class="py-name" href="#" onclick="return doclink('link-123', 'viz', 'link-122');">viz</a></tt> </tt>
<a name="L709"></a><tt class="py-lineno"> 709</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L710"></a><tt class="py-lineno"> 710</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="trunk.BIP.SDE.gillespie.viz" class="py-name" href="#" onclick="return doclink('link-124', 'viz', 'link-122');">viz</a></tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L711"></a><tt class="py-lineno"> 711</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L712"></a><tt class="py-lineno"> 712</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">every_run_plot</tt> <tt class="py-op">=</tt> <tt class="py-name">xmlrpclib</tt><tt class="py-op">.</tt><tt class="py-name">ServerProxy</tt><tt class="py-op">(</tt><tt class="py-string">'http://localhost:%s'</tt><tt class="py-op">%</tt><tt id="link-125" class="py-name"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-125', 'rpc_plot', 'link-12');">rpc_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">hold</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">allow_none</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L713"></a><tt class="py-lineno"> 713</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.po()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#po"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-126', 'po', 'link-126');">po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#pool of processes for parallel processing</tt> </tt>
</div><a name="L714"></a><tt class="py-lineno"> 714</tt>  <tt class="py-line">     </tt>
<a name="Meld.current_plot"></a><div id="Meld.current_plot-def"><a name="L715"></a><tt class="py-lineno"> 715</tt> <a class="py-toggle" href="#" id="Meld.current_plot-toggle" onclick="return toggle('Meld.current_plot');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#current_plot">current_plot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">series</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">idx</tt><tt class="py-op">,</tt> <tt class="py-param">vars</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">step</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.current_plot-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.current_plot-expanded"><a name="L716"></a><tt class="py-lineno"> 716</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L717"></a><tt class="py-lineno"> 717</tt>  <tt class="py-line"><tt class="py-docstring">        Plots the last simulated series</tt> </tt>
<a name="L718"></a><tt class="py-lineno"> 718</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L719"></a><tt class="py-lineno"> 719</tt>  <tt class="py-line"><tt class="py-docstring">         :Parameters:</tt> </tt>
<a name="L720"></a><tt class="py-lineno"> 720</tt>  <tt class="py-line"><tt class="py-docstring">            - `series`: Record array with the simulated series.</tt> </tt>
<a name="L721"></a><tt class="py-lineno"> 721</tt>  <tt class="py-line"><tt class="py-docstring">            - `idx`: Integer index of the curve to plot .</tt> </tt>
<a name="L722"></a><tt class="py-lineno"> 722</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Dictionary with the full dataset.</tt> </tt>
<a name="L723"></a><tt class="py-lineno"> 723</tt>  <tt class="py-line"><tt class="py-docstring">            - `vars`: List with variable names to be plotted.</tt> </tt>
<a name="L724"></a><tt class="py-lineno"> 724</tt>  <tt class="py-line"><tt class="py-docstring">            - `step`: Step of the chain</tt> </tt>
<a name="L725"></a><tt class="py-lineno"> 725</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L726"></a><tt class="py-lineno"> 726</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L727"></a><tt class="py-lineno"> 727</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastidx</tt> <tt class="py-op">==</tt> <tt class="py-name">idx</tt><tt class="py-op">:</tt> </tt>
<a name="L728"></a><tt class="py-lineno"> 728</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> </tt>
<a name="L729"></a><tt class="py-lineno"> 729</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L730"></a><tt class="py-lineno"> 730</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L731"></a><tt class="py-lineno"> 731</tt>  <tt class="py-line">        <tt class="py-comment">#print series.shape, idx</tt> </tt>
<a name="L732"></a><tt class="py-lineno"> 732</tt>  <tt class="py-line">        <tt class="py-name">best_series</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L733"></a><tt class="py-lineno"> 733</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L734"></a><tt class="py-lineno"> 734</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">every_run_plot</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Best fit. Last updated on %s"</tt><tt class="py-op">%</tt><tt id="link-127" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream.step()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#step,Method trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step()=trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#step"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-127', 'step', 'link-127');">step</a></tt><tt class="py-op">,</tt> <tt class="py-string">'points'</tt> <tt class="py-op">)</tt> </tt>
<a name="L735"></a><tt class="py-lineno"> 735</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">every_run_plot</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">best_series</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Best fit. Last updated on %s"</tt><tt class="py-op">%</tt><tt id="link-128" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-128', 'step', 'link-127');">step</a></tt><tt class="py-op">,</tt> <tt class="py-string">'lines'</tt> <tt class="py-op">)</tt> </tt>
<a name="L736"></a><tt class="py-lineno"> 736</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">every_run_plot</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-129', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L737"></a><tt class="py-lineno"> 737</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastidx</tt> <tt class="py-op">=</tt> <tt class="py-name">idx</tt> </tt>
</div><a name="L738"></a><tt class="py-lineno"> 738</tt>  <tt class="py-line">     </tt>
<a name="Meld.setPhi"></a><div id="Meld.setPhi-def"><a name="L739"></a><tt class="py-lineno"> 739</tt> <a class="py-toggle" href="#" id="Meld.setPhi-toggle" onclick="return toggle('Meld.setPhi');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#setPhi">setPhi</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">,</tt> <tt class="py-param">dists</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">norm</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">limits</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setPhi-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.setPhi-expanded"><a name="L740"></a><tt class="py-lineno"> 740</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L741"></a><tt class="py-lineno"> 741</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the models Outputs, or Phi, and generate the samples from prior distributions </tt> </tt>
<a name="L742"></a><tt class="py-lineno"> 742</tt>  <tt class="py-line"><tt class="py-docstring">        needed for the melding replicates.</tt> </tt>
<a name="L743"></a><tt class="py-lineno"> 743</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L744"></a><tt class="py-lineno"> 744</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L745"></a><tt class="py-lineno"> 745</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the variables.</tt> </tt>
<a name="L746"></a><tt class="py-lineno"> 746</tt>  <tt class="py-line"><tt class="py-docstring">            - `dists`: is a list of RNG from scipy.stats</tt> </tt>
<a name="L747"></a><tt class="py-lineno"> 747</tt>  <tt class="py-line"><tt class="py-docstring">            - `pars`: is a list of tuples of variables for each prior distribution, respectively.</tt> </tt>
<a name="L748"></a><tt class="py-lineno"> 748</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: lower and upper limits on the support of variables.</tt> </tt>
<a name="L749"></a><tt class="py-lineno"> 749</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L750"></a><tt class="py-lineno"> 750</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">:</tt> </tt>
<a name="L751"></a><tt class="py-lineno"> 751</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Number of names(%s) does not match the number of output variables(%s)."</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L752"></a><tt class="py-lineno"> 752</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L753"></a><tt class="py-lineno"> 753</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L754"></a><tt class="py-lineno"> 754</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L755"></a><tt class="py-lineno"> 755</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plimits</tt> <tt class="py-op">=</tt> <tt class="py-name">limits</tt> </tt>
<a name="L756"></a><tt class="py-lineno"> 756</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phipars</tt> <tt class="py-op">=</tt> <tt class="py-name">pars</tt> </tt>
<a name="L757"></a><tt class="py-lineno"> 757</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">dists</tt><tt class="py-op">,</tt><tt class="py-name">pars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L758"></a><tt class="py-lineno"> 758</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-130" class="py-name"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-130', 'lhs', 'link-2');">lhs</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-131', 'lhs', 'link-2');">lhs</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L759"></a><tt class="py-lineno"> 759</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2type</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">)</tt> </tt>
<a name="L760"></a><tt class="py-lineno"> 760</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi_dists</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">d</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> </tt>
</div><a name="L761"></a><tt class="py-lineno"> 761</tt>  <tt class="py-line"> </tt>
<a name="L762"></a><tt class="py-lineno"> 762</tt>  <tt class="py-line"> </tt>
<a name="L763"></a><tt class="py-lineno"> 763</tt>  <tt class="py-line">         </tt>
<a name="Meld.setTheta"></a><div id="Meld.setTheta-def"><a name="L764"></a><tt class="py-lineno"> 764</tt> <a class="py-toggle" href="#" id="Meld.setTheta-toggle" onclick="return toggle('Meld.setTheta');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#setTheta">setTheta</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">,</tt> <tt class="py-param">dists</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">norm</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">lims</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setTheta-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.setTheta-expanded"><a name="L765"></a><tt class="py-lineno"> 765</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L766"></a><tt class="py-lineno"> 766</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the models inputs and generate the samples from prior distributions </tt> </tt>
<a name="L767"></a><tt class="py-lineno"> 767</tt>  <tt class="py-line"><tt class="py-docstring">        needed for the dists the melding replicates.</tt> </tt>
<a name="L768"></a><tt class="py-lineno"> 768</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L769"></a><tt class="py-lineno"> 769</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L770"></a><tt class="py-lineno"> 770</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the parameters.</tt> </tt>
<a name="L771"></a><tt class="py-lineno"> 771</tt>  <tt class="py-line"><tt class="py-docstring">            - `dists`: is a list of RNG from scipy.stats</tt> </tt>
<a name="L772"></a><tt class="py-lineno"> 772</tt>  <tt class="py-line"><tt class="py-docstring">            - `pars`: is a list of tuples of parameters for each prior distribution, respectivelydists</tt> </tt>
<a name="L773"></a><tt class="py-lineno"> 773</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L774"></a><tt class="py-lineno"> 774</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L775"></a><tt class="py-lineno"> 775</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L776"></a><tt class="py-lineno"> 776</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetapars</tt> <tt class="py-op">=</tt> <tt class="py-name">pars</tt> </tt>
<a name="L777"></a><tt class="py-lineno"> 777</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlimits</tt> <tt class="py-op">=</tt> <tt class="py-name">lims</tt> </tt>
<a name="L778"></a><tt class="py-lineno"> 778</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L779"></a><tt class="py-lineno"> 779</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L780"></a><tt class="py-lineno"> 780</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L781"></a><tt class="py-lineno"> 781</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">dists</tt><tt class="py-op">,</tt><tt class="py-name">pars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L782"></a><tt class="py-lineno"> 782</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-132" class="py-name"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-132', 'lhs', 'link-2');">lhs</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-133', 'lhs', 'link-2');">lhs</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L783"></a><tt class="py-lineno"> 783</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">d</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> </tt>
</div><a name="L784"></a><tt class="py-lineno"> 784</tt>  <tt class="py-line">         </tt>
<a name="Meld.add_salt"></a><div id="Meld.add_salt-def"><a name="L785"></a><tt class="py-lineno"> 785</tt> <a class="py-toggle" href="#" id="Meld.add_salt-toggle" onclick="return toggle('Meld.add_salt');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#add_salt">add_salt</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">dataset</tt><tt class="py-op">,</tt><tt class="py-param">band</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.add_salt-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.add_salt-expanded"><a name="L786"></a><tt class="py-lineno"> 786</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L787"></a><tt class="py-lineno"> 787</tt>  <tt class="py-line"><tt class="py-docstring">        Adds a few extra uniformly distributed data </tt> </tt>
<a name="L788"></a><tt class="py-lineno"> 788</tt>  <tt class="py-line"><tt class="py-docstring">        points beyond the dataset range.</tt> </tt>
<a name="L789"></a><tt class="py-lineno"> 789</tt>  <tt class="py-line"><tt class="py-docstring">        This is done by adding from a uniform dist.</tt> </tt>
<a name="L790"></a><tt class="py-lineno"> 790</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L791"></a><tt class="py-lineno"> 791</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L792"></a><tt class="py-lineno"> 792</tt>  <tt class="py-line"><tt class="py-docstring">            - `dataset`: vector of data</tt> </tt>
<a name="L793"></a><tt class="py-lineno"> 793</tt>  <tt class="py-line"><tt class="py-docstring">            - `band`: Fraction of range to extend [0,1[</tt> </tt>
<a name="L794"></a><tt class="py-lineno"> 794</tt>  <tt class="py-line"><tt class="py-docstring">            </tt> </tt>
<a name="L795"></a><tt class="py-lineno"> 795</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L796"></a><tt class="py-lineno"> 796</tt>  <tt class="py-line"><tt class="py-docstring">            Salted dataset.</tt> </tt>
<a name="L797"></a><tt class="py-lineno"> 797</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L798"></a><tt class="py-lineno"> 798</tt>  <tt class="py-line">        <tt class="py-name">dmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">)</tt> </tt>
<a name="L799"></a><tt class="py-lineno"> 799</tt>  <tt class="py-line">        <tt class="py-name">dmin</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">)</tt> </tt>
<a name="L800"></a><tt class="py-lineno"> 800</tt>  <tt class="py-line">        <tt class="py-name">drange</tt> <tt class="py-op">=</tt> <tt class="py-name">dmax</tt><tt class="py-op">-</tt><tt class="py-name">dmin</tt> </tt>
<a name="L801"></a><tt class="py-lineno"> 801</tt>  <tt class="py-line">        <tt class="py-name">hb</tt> <tt class="py-op">=</tt> <tt class="py-name">drange</tt><tt class="py-op">*</tt><tt class="py-name">band</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L802"></a><tt class="py-lineno"> 802</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">concatenate</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">(</tt><tt class="py-name">dmin</tt><tt class="py-op">-</tt><tt class="py-name">hb</tt><tt class="py-op">,</tt><tt class="py-name">dmax</tt><tt class="py-op">-</tt><tt class="py-name">dmin</tt><tt class="py-op">+</tt><tt class="py-name">hb</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">*</tt><tt class="py-number">.05</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L803"></a><tt class="py-lineno"> 803</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div><a name="L804"></a><tt class="py-lineno"> 804</tt>  <tt class="py-line">     </tt>
<a name="Meld.setThetaFromData"></a><div id="Meld.setThetaFromData-def"><a name="L805"></a><tt class="py-lineno"> 805</tt> <a class="py-toggle" href="#" id="Meld.setThetaFromData-toggle" onclick="return toggle('Meld.setThetaFromData');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#setThetaFromData">setThetaFromData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setThetaFromData-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.setThetaFromData-expanded"><a name="L806"></a><tt class="py-lineno"> 806</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L807"></a><tt class="py-lineno"> 807</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the model inputs and set the prior distributions from the vectors</tt> </tt>
<a name="L808"></a><tt class="py-lineno"> 808</tt>  <tt class="py-line"><tt class="py-docstring">        in data.</tt> </tt>
<a name="L809"></a><tt class="py-lineno"> 809</tt>  <tt class="py-line"><tt class="py-docstring">        This method is to be used when the prior distributions are available in </tt> </tt>
<a name="L810"></a><tt class="py-lineno"> 810</tt>  <tt class="py-line"><tt class="py-docstring">        the form of a sample from an empirical distribution such as a bayesian</tt> </tt>
<a name="L811"></a><tt class="py-lineno"> 811</tt>  <tt class="py-line"><tt class="py-docstring">        posterior.</tt> </tt>
<a name="L812"></a><tt class="py-lineno"> 812</tt>  <tt class="py-line"><tt class="py-docstring">        In order to expand the samples provided, K samples are generated from a</tt> </tt>
<a name="L813"></a><tt class="py-lineno"> 813</tt>  <tt class="py-line"><tt class="py-docstring">        kernel density estimate of the original sample.</tt> </tt>
<a name="L814"></a><tt class="py-lineno"> 814</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L815"></a><tt class="py-lineno"> 815</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L816"></a><tt class="py-lineno"> 816</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the parameters.</tt> </tt>
<a name="L817"></a><tt class="py-lineno"> 817</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: list of vectors. Samples of a proposed distribution</tt> </tt>
<a name="L818"></a><tt class="py-lineno"> 818</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: List of (min,max) tuples for each theta to make sure samples are not generated outside these limits.</tt> </tt>
<a name="L819"></a><tt class="py-lineno"> 819</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L820"></a><tt class="py-lineno"> 820</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L821"></a><tt class="py-lineno"> 821</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L822"></a><tt class="py-lineno"> 822</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlimits</tt> <tt class="py-op">=</tt> <tt class="py-name">limits</tt> </tt>
<a name="L823"></a><tt class="py-lineno"> 823</tt>  <tt class="py-line">        <tt class="py-name">tlimits</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">limits</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L824"></a><tt class="py-lineno"> 824</tt>  <tt class="py-line">        <tt class="py-keyword">class</tt> <tt class="py-def-name">Proposal</tt><tt class="py-op">:</tt> </tt>
<a name="L825"></a><tt class="py-lineno"> 825</tt>  <tt class="py-line">            <tt class="py-docstring">"class wrapping a kde adding similar interface to stats dists"</tt> </tt>
<a name="L826"></a><tt class="py-lineno"> 826</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">__init__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">dist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L827"></a><tt class="py-lineno"> 827</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt> <tt class="py-op">=</tt> <tt class="py-name">name</tt> </tt>
<a name="L828"></a><tt class="py-lineno"> 828</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">dist</tt> </tt>
</div><a name="L829"></a><tt class="py-lineno"> 829</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">__call__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L830"></a><tt class="py-lineno"> 830</tt>  <tt class="py-line">                <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> </tt>
<a name="L831"></a><tt class="py-lineno"> 831</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">&gt;=</tt><tt class="py-name">tlimits</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">smp</tt><tt class="py-op">&lt;=</tt><tt class="py-name">tlimits</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L832"></a><tt class="py-lineno"> 832</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L833"></a><tt class="py-lineno"> 833</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">smp</tt> </tt>
</div><a name="L834"></a><tt class="py-lineno"> 834</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">rvs</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L835"></a><tt class="py-lineno"> 835</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-string">'size'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwds</tt><tt class="py-op">:</tt> </tt>
<a name="L836"></a><tt class="py-lineno"> 836</tt>  <tt class="py-line">                    <tt class="py-name">sz</tt> <tt class="py-op">=</tt> <tt class="py-name">kwds</tt><tt class="py-op">[</tt><tt class="py-string">'size'</tt><tt class="py-op">]</tt> </tt>
<a name="L837"></a><tt class="py-lineno"> 837</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L838"></a><tt class="py-lineno"> 838</tt>  <tt class="py-line">                    <tt class="py-name">sz</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L839"></a><tt class="py-lineno"> 839</tt>  <tt class="py-line">                    <tt class="py-comment">#TODO implement return of multiple samples here if necessary</tt> </tt>
<a name="L840"></a><tt class="py-lineno"> 840</tt>  <tt class="py-line">                <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> </tt>
<a name="L841"></a><tt class="py-lineno"> 841</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">&gt;=</tt><tt class="py-name">tlimits</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">smp</tt><tt class="py-op">&lt;=</tt><tt class="py-name">tlimits</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L842"></a><tt class="py-lineno"> 842</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-name">sz</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L843"></a><tt class="py-lineno"> 843</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">smp</tt> </tt>
</div><a name="L844"></a><tt class="py-lineno"> 844</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">stats</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">moments</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L845"></a><tt class="py-lineno"> 845</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">rv_continuous</tt><tt class="py-op">,</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">rv_discrete</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L846"></a><tt class="py-lineno"> 846</tt>  <tt class="py-line">                    <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt><tt class="py-op">(</tt><tt class="py-name">moments</tt><tt class="py-op">=</tt><tt class="py-string">'m'</tt><tt class="py-op">)</tt> </tt>
<a name="L847"></a><tt class="py-lineno"> 847</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L848"></a><tt class="py-lineno"> 848</tt>  <tt class="py-line">                    <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">dataset</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L849"></a><tt class="py-lineno"> 849</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">pdf</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L850"></a><tt class="py-lineno"> 850</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L851"></a><tt class="py-lineno"> 851</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">pmf</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L852"></a><tt class="py-lineno"> 852</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L853"></a><tt class="py-lineno"> 853</tt>  <tt class="py-line">                 </tt>
<a name="L854"></a><tt class="py-lineno"> 854</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L855"></a><tt class="py-lineno"> 855</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L856"></a><tt class="py-lineno"> 856</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L857"></a><tt class="py-lineno"> 857</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">lim</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L858"></a><tt class="py-lineno"> 858</tt>  <tt class="py-line">                <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L859"></a><tt class="py-lineno"> 859</tt>  <tt class="py-line">                <tt class="py-comment">#add some points uniformly across the support </tt> </tt>
<a name="L860"></a><tt class="py-lineno"> 860</tt>  <tt class="py-line">                <tt class="py-comment">#to help MCMC to escape from prior bounds</tt> </tt>
<a name="L861"></a><tt class="py-lineno"> 861</tt>  <tt class="py-line">                <tt class="py-name">salted</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.add_salt()=trunk.BIP.Bayes.Melding.Meld-class.html#add_salt"><a title="trunk.BIP.Bayes.Melding.Meld.add_salt" class="py-name" href="#" onclick="return doclink('link-134', 'add_salt', 'link-134');">add_salt</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt><tt class="py-op">)</tt> </tt>
<a name="L862"></a><tt class="py-lineno"> 862</tt>  <tt class="py-line"> </tt>
<a name="L863"></a><tt class="py-lineno"> 863</tt>  <tt class="py-line">                <tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">salted</tt><tt class="py-op">)</tt> </tt>
<a name="L864"></a><tt class="py-lineno"> 864</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">:</tt> </tt>
<a name="L865"></a><tt class="py-lineno"> 865</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">lim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">lim</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L866"></a><tt class="py-lineno"> 866</tt>  <tt class="py-line">                <tt class="py-comment">#print self.q1theta[n].shape, array(smp[:self.K]).shape</tt> </tt>
<a name="L867"></a><tt class="py-lineno"> 867</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L868"></a><tt class="py-lineno"> 868</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">Proposal</tt><tt class="py-op">(</tt><tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">dist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L869"></a><tt class="py-lineno"> 869</tt>  <tt class="py-line"> </tt>
<a name="Meld.setPhiFromData"></a><div id="Meld.setPhiFromData-def"><a name="L870"></a><tt class="py-lineno"> 870</tt> <a class="py-toggle" href="#" id="Meld.setPhiFromData-toggle" onclick="return toggle('Meld.setPhiFromData');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#setPhiFromData">setPhiFromData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setPhiFromData-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.setPhiFromData-expanded"><a name="L871"></a><tt class="py-lineno"> 871</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L872"></a><tt class="py-lineno"> 872</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the model outputs and set their prior distributions from the</tt> </tt>
<a name="L873"></a><tt class="py-lineno"> 873</tt>  <tt class="py-line"><tt class="py-docstring">        vectors in data.</tt> </tt>
<a name="L874"></a><tt class="py-lineno"> 874</tt>  <tt class="py-line"><tt class="py-docstring">        This method is to be used when the prior distributions are available in</tt> </tt>
<a name="L875"></a><tt class="py-lineno"> 875</tt>  <tt class="py-line"><tt class="py-docstring">        the form of a sample from an empirical distribution such as a bayesian</tt> </tt>
<a name="L876"></a><tt class="py-lineno"> 876</tt>  <tt class="py-line"><tt class="py-docstring">        posterior.</tt> </tt>
<a name="L877"></a><tt class="py-lineno"> 877</tt>  <tt class="py-line"><tt class="py-docstring">        In order to expand the samples provided, K samples are generated from a</tt> </tt>
<a name="L878"></a><tt class="py-lineno"> 878</tt>  <tt class="py-line"><tt class="py-docstring">        kernel density estimate of the original sample.</tt> </tt>
<a name="L879"></a><tt class="py-lineno"> 879</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L880"></a><tt class="py-lineno"> 880</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L881"></a><tt class="py-lineno"> 881</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the variables.</tt> </tt>
<a name="L882"></a><tt class="py-lineno"> 882</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: list of vectors. Samples of the proposed distribution.</tt> </tt>
<a name="L883"></a><tt class="py-lineno"> 883</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: list of tuples (ll,ul),lower and upper limits on the support of variables.</tt> </tt>
<a name="L884"></a><tt class="py-lineno"> 884</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L885"></a><tt class="py-lineno"> 885</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L886"></a><tt class="py-lineno"> 886</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L887"></a><tt class="py-lineno"> 887</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L888"></a><tt class="py-lineno"> 888</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">limits</tt> <tt class="py-op">=</tt> <tt class="py-name">limits</tt> </tt>
<a name="L889"></a><tt class="py-lineno"> 889</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L890"></a><tt class="py-lineno"> 890</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L891"></a><tt class="py-lineno"> 891</tt>  <tt class="py-line">            <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L892"></a><tt class="py-lineno"> 892</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">:</tt> </tt>
<a name="L893"></a><tt class="py-lineno"> 893</tt>  <tt class="py-line">                <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L894"></a><tt class="py-lineno"> 894</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">limits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">limits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L895"></a><tt class="py-lineno"> 895</tt>  <tt class="py-line">                <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L896"></a><tt class="py-lineno"> 896</tt>  <tt class="py-line">                    <tt class="py-comment">#d is has no variation, i.e., all elements are the same</tt> </tt>
<a name="L897"></a><tt class="py-lineno"> 897</tt>  <tt class="py-line">                    <tt class="py-comment">#print d</tt> </tt>
<a name="L898"></a><tt class="py-lineno"> 898</tt>  <tt class="py-line">                    <tt class="py-comment">#raise LinAlgError, "Singular matrix"</tt> </tt>
<a name="L899"></a><tt class="py-lineno"> 899</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">d</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-comment">#in this case return a constant sample</tt> </tt>
<a name="L900"></a><tt class="py-lineno"> 900</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L901"></a><tt class="py-lineno"> 901</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2type</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">'empirical'</tt><tt class="py-op">)</tt> </tt>
<a name="L902"></a><tt class="py-lineno"> 902</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L903"></a><tt class="py-lineno"> 903</tt>  <tt class="py-line">        <tt class="py-comment">#self.q2phi = self.filtM(self.q2phi, self.q2phi, limits)</tt> </tt>
<a name="L904"></a><tt class="py-lineno"> 904</tt>  <tt class="py-line"> </tt>
<a name="L905"></a><tt class="py-lineno"> 905</tt>  <tt class="py-line">         </tt>
<a name="Meld.run"></a><div id="Meld.run-def"><a name="L906"></a><tt class="py-lineno"> 906</tt> <a class="py-toggle" href="#" id="Meld.run-toggle" onclick="return toggle('Meld.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.run-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.run-expanded"><a name="L907"></a><tt class="py-lineno"> 907</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L908"></a><tt class="py-lineno"> 908</tt>  <tt class="py-line"><tt class="py-docstring">        Runs the model through the Melding inference.model</tt> </tt>
<a name="L909"></a><tt class="py-lineno"> 909</tt>  <tt class="py-line"><tt class="py-docstring">        model is a callable which return the output of the deterministic model,</tt> </tt>
<a name="L910"></a><tt class="py-lineno"> 910</tt>  <tt class="py-line"><tt class="py-docstring">        i.e. the model itself.</tt> </tt>
<a name="L911"></a><tt class="py-lineno"> 911</tt>  <tt class="py-line"><tt class="py-docstring">        The model is run self.K times to obtain phi = M(theta).</tt> </tt>
<a name="L912"></a><tt class="py-lineno"> 912</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L913"></a><tt class="py-lineno"> 913</tt>  <tt class="py-line">        <tt class="py-comment">#TODO: implement calculation of AIC,BIC and DIC for SIR</tt> </tt>
<a name="L914"></a><tt class="py-lineno"> 914</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L915"></a><tt class="py-lineno"> 915</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L916"></a><tt class="py-lineno"> 916</tt>  <tt class="py-line">            <tt id="link-135" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-135', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-136', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-137', 'model', 'link-22');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L917"></a><tt class="py-lineno"> 917</tt>  <tt class="py-line">            <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt id="link-138" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-138', 'r', 'link-64');">r</a></tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L918"></a><tt class="py-lineno"> 918</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">=</tt> <tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-comment">#self.model(*theta)[-1] #phi is the last point in the simulation</tt> </tt>
<a name="L919"></a><tt class="py-lineno"> 919</tt>  <tt class="py-line"> </tt>
<a name="L920"></a><tt class="py-lineno"> 920</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L921"></a><tt class="py-lineno"> 921</tt>  <tt class="py-line">         </tt>
<a name="Meld.getPosteriors"></a><div id="Meld.getPosteriors-def"><a name="L922"></a><tt class="py-lineno"> 922</tt> <a class="py-toggle" href="#" id="Meld.getPosteriors-toggle" onclick="return toggle('Meld.getPosteriors');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#getPosteriors">getPosteriors</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">t</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.getPosteriors-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.getPosteriors-expanded"><a name="L923"></a><tt class="py-lineno"> 923</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L924"></a><tt class="py-lineno"> 924</tt>  <tt class="py-line"><tt class="py-docstring">        Updates the posteriors of the model's output for the last t time steps.</tt> </tt>
<a name="L925"></a><tt class="py-lineno"> 925</tt>  <tt class="py-line"><tt class="py-docstring">        Returns two record arrays:</tt> </tt>
<a name="L926"></a><tt class="py-lineno"> 926</tt>  <tt class="py-line"><tt class="py-docstring">        - The posteriors of the Theta</tt> </tt>
<a name="L927"></a><tt class="py-lineno"> 927</tt>  <tt class="py-line"><tt class="py-docstring">        - the posterior of Phi last t values of time-series. self.L by `t` arrays.</tt> </tt>
<a name="L928"></a><tt class="py-lineno"> 928</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L929"></a><tt class="py-lineno"> 929</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L930"></a><tt class="py-lineno"> 930</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the posterior time-series to return.</tt> </tt>
<a name="L931"></a><tt class="py-lineno"> 931</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L932"></a><tt class="py-lineno"> 932</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt><tt class="py-op">:</tt> </tt>
<a name="L933"></a><tt class="py-lineno"> 933</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"Estimation has not yet been run"</tt> </tt>
<a name="L934"></a><tt class="py-lineno"> 934</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L935"></a><tt class="py-lineno"> 935</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L936"></a><tt class="py-lineno"> 936</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> </tt>
<a name="L937"></a><tt class="py-lineno"> 937</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L938"></a><tt class="py-lineno"> 938</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">cb</tt><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L939"></a><tt class="py-lineno"> 939</tt>  <tt class="py-line">            <tt class="py-docstring">'''</tt> </tt>
<a name="L940"></a><tt class="py-lineno"> 940</tt>  <tt class="py-line"><tt class="py-docstring">            callback function for the asynchronous model runs.</tt> </tt>
<a name="L941"></a><tt class="py-lineno"> 941</tt>  <tt class="py-line"><tt class="py-docstring">            r: tuple with results of simulation (results, run#)</tt> </tt>
<a name="L942"></a><tt class="py-lineno"> 942</tt>  <tt class="py-line"><tt class="py-docstring">            '''</tt> </tt>
<a name="L943"></a><tt class="py-lineno"> 943</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L944"></a><tt class="py-lineno"> 944</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">[</tt><tt id="link-139" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-139', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-140" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-140', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L945"></a><tt class="py-lineno"> 945</tt>  <tt class="py-line">                <tt class="py-comment">#self.post_phi[r[1]]= [tuple(l) for l in r[0][-t:]]</tt> </tt>
<a name="L946"></a><tt class="py-lineno"> 946</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L947"></a><tt class="py-lineno"> 947</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">[</tt><tt id="link-141" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-141', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt id="link-142" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-142', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
</div><a name="L948"></a><tt class="py-lineno"> 948</tt>  <tt class="py-line">        <tt id="link-143" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-143', 'po', 'link-126');">po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L949"></a><tt class="py-lineno"> 949</tt>  <tt class="py-line">        <tt class="py-comment">#random indices for the marginal posteriors of theta</tt> </tt>
<a name="L950"></a><tt class="py-lineno"> 950</tt>  <tt class="py-line">        <tt class="py-name">pti</tt> <tt class="py-op">=</tt> <tt id="link-144" class="py-name"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-144', 'lhs', 'link-2');">lhs</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="trunk.BIP.Bayes.lhs
trunk.BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-145', 'lhs', 'link-2');">lhs</a></tt><tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">randint</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">siz</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L951"></a><tt class="py-lineno"> 951</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment">#Monte Carlo with values of the posterior of Theta</tt> </tt>
<a name="L952"></a><tt class="py-lineno"> 952</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">pti</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L953"></a><tt class="py-lineno"> 953</tt>  <tt class="py-line">            <tt id="link-146" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-146', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-147" class="py-name" targets="Function trunk.BIP.Bayes.Melding.enumRun()=trunk.BIP.Bayes.Melding-module.html#enumRun"><a title="trunk.BIP.Bayes.Melding.enumRun" class="py-name" href="#" onclick="return doclink('link-147', 'enumRun', 'link-147');">enumRun</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-148', 'model', 'link-22');">model</a></tt><tt class="py-op">,</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">callback</tt><tt class="py-op">=</tt><tt class="py-name">cb</tt><tt class="py-op">)</tt> </tt>
<a name="L954"></a><tt class="py-lineno"> 954</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L955"></a><tt class="py-lineno"> 955</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; L = %s\r"</tt><tt class="py-op">%</tt><tt class="py-name">i</tt> </tt>
<a name="L956"></a><tt class="py-lineno"> 956</tt>  <tt class="py-line"> </tt>
<a name="L957"></a><tt class="py-lineno"> 957</tt>  <tt class="py-line">        <tt id="link-149" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-149', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L958"></a><tt class="py-lineno"> 958</tt>  <tt class="py-line">        <tt id="link-150" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-150', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L959"></a><tt class="py-lineno"> 959</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> </tt>
</div><a name="L960"></a><tt class="py-lineno"> 960</tt>  <tt class="py-line"> </tt>
<a name="Meld.filtM"></a><div id="Meld.filtM-def"><a name="L961"></a><tt class="py-lineno"> 961</tt> <a class="py-toggle" href="#" id="Meld.filtM-toggle" onclick="return toggle('Meld.filtM');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#filtM">filtM</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">cond</tt><tt class="py-op">,</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.filtM-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.filtM-expanded"><a name="L962"></a><tt class="py-lineno"> 962</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L963"></a><tt class="py-lineno"> 963</tt>  <tt class="py-line"><tt class="py-docstring">        Multiple condition filtering.</tt> </tt>
<a name="L964"></a><tt class="py-lineno"> 964</tt>  <tt class="py-line"><tt class="py-docstring">        Remove values in x[i], if corresponding values in</tt> </tt>
<a name="L965"></a><tt class="py-lineno"> 965</tt>  <tt class="py-line"><tt class="py-docstring">        cond[i] are less than limits[i][0] or greater than</tt> </tt>
<a name="L966"></a><tt class="py-lineno"> 966</tt>  <tt class="py-line"><tt class="py-docstring">        limits[i][1].</tt> </tt>
<a name="L967"></a><tt class="py-lineno"> 967</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L968"></a><tt class="py-lineno"> 968</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L969"></a><tt class="py-lineno"> 969</tt>  <tt class="py-line"><tt class="py-docstring">            - `cond`: is an array of conditions.</tt> </tt>
<a name="L970"></a><tt class="py-lineno"> 970</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: is a list of tuples (ll,ul) with length equal to number of lines in `cond` and `x`.</tt> </tt>
<a name="L971"></a><tt class="py-lineno"> 971</tt>  <tt class="py-line"><tt class="py-docstring">            - `x`: array to be filtered.</tt> </tt>
<a name="L972"></a><tt class="py-lineno"> 972</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L973"></a><tt class="py-lineno"> 973</tt>  <tt class="py-line">        <tt class="py-comment"># Deconstruct the record array, if necessary.</tt> </tt>
<a name="L974"></a><tt class="py-lineno"> 974</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L975"></a><tt class="py-lineno"> 975</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">,</tt> <tt class="py-name">recarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L976"></a><tt class="py-lineno"> 976</tt>  <tt class="py-line">            <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L977"></a><tt class="py-lineno"> 977</tt>  <tt class="py-line">            <tt class="py-name">cond</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">cond</tt><tt class="py-op">[</tt><tt class="py-name">v</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cond</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L978"></a><tt class="py-lineno"> 978</tt>  <tt class="py-line">            <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">v</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L979"></a><tt class="py-lineno"> 979</tt>  <tt class="py-line"> </tt>
<a name="L980"></a><tt class="py-lineno"> 980</tt>  <tt class="py-line">        <tt class="py-name">cond</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">)</tt> </tt>
<a name="L981"></a><tt class="py-lineno"> 981</tt>  <tt class="py-line">        <tt class="py-name">cnd</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt> </tt>
<a name="L982"></a><tt class="py-lineno"> 982</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">,</tt><tt class="py-name">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L983"></a><tt class="py-lineno"> 983</tt>  <tt class="py-line">            <tt class="py-name">ll</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L984"></a><tt class="py-lineno"> 984</tt>  <tt class="py-line">            <tt class="py-name">ul</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L985"></a><tt class="py-lineno"> 985</tt>  <tt class="py-line">            <tt class="py-comment">#print cond.shape,cnd.shape,i.shape,ll,ul</tt> </tt>
<a name="L986"></a><tt class="py-lineno"> 986</tt>  <tt class="py-line">            <tt class="py-name">cnd</tt> <tt class="py-op">=</tt> <tt class="py-name">cnd</tt> <tt class="py-op">&amp;</tt> <tt class="py-name">less</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">ul</tt><tt class="py-op">)</tt> <tt class="py-op">&amp;</tt> <tt class="py-name">greater</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">ll</tt><tt class="py-op">)</tt> </tt>
<a name="L987"></a><tt class="py-lineno"> 987</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">compress</tt><tt class="py-op">(</tt><tt class="py-name">cnd</tt><tt class="py-op">,</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L988"></a><tt class="py-lineno"> 988</tt>  <tt class="py-line"> </tt>
<a name="L989"></a><tt class="py-lineno"> 989</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt><tt class="py-comment">#Reconstruct the record array</tt> </tt>
<a name="L990"></a><tt class="py-lineno"> 990</tt>  <tt class="py-line">            <tt id="link-151" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-151', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L991"></a><tt class="py-lineno"> 991</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L992"></a><tt class="py-lineno"> 992</tt>  <tt class="py-line">                <tt id="link-152" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-152', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">f</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L993"></a><tt class="py-lineno"> 993</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">=</tt><tt id="link-153" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-153', 'r', 'link-64');">r</a></tt> </tt>
<a name="L994"></a><tt class="py-lineno"> 994</tt>  <tt class="py-line"> </tt>
<a name="L995"></a><tt class="py-lineno"> 995</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">f</tt> </tt>
</div><a name="L996"></a><tt class="py-lineno"> 996</tt>  <tt class="py-line"> </tt>
<a name="L997"></a><tt class="py-lineno"> 997</tt>  <tt class="py-line">         </tt>
<a name="L998"></a><tt class="py-lineno"> 998</tt>  <tt class="py-line"> </tt>
<a name="Meld.logPooling"></a><div id="Meld.logPooling-def"><a name="L999"></a><tt class="py-lineno"> 999</tt> <a class="py-toggle" href="#" id="Meld.logPooling-toggle" onclick="return toggle('Meld.logPooling');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#logPooling">logPooling</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">phi</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.logPooling-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.logPooling-expanded"><a name="L1000"></a><tt class="py-lineno">1000</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1001"></a><tt class="py-lineno">1001</tt>  <tt class="py-line"><tt class="py-docstring">        Returns the probability associated with each phi[i]</tt> </tt>
<a name="L1002"></a><tt class="py-lineno">1002</tt>  <tt class="py-line"><tt class="py-docstring">        on the pooled pdf of phi and q2phi.</tt> </tt>
<a name="L1003"></a><tt class="py-lineno">1003</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1004"></a><tt class="py-lineno">1004</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L1005"></a><tt class="py-lineno">1005</tt>  <tt class="py-line"><tt class="py-docstring">            - `phi`: prior of Phi induced by the model and q1theta.</tt> </tt>
<a name="L1006"></a><tt class="py-lineno">1006</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1007"></a><tt class="py-lineno">1007</tt>  <tt class="py-line">         </tt>
<a name="L1008"></a><tt class="py-lineno">1008</tt>  <tt class="py-line"><tt class="py-comment">#       Estimating the multivariate joint probability densities</tt> </tt>
<a name="L1009"></a><tt class="py-lineno">1009</tt>  <tt class="py-line">        <tt class="py-name">phidens</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1010"></a><tt class="py-lineno">1010</tt>  <tt class="py-line"> </tt>
<a name="L1011"></a><tt class="py-lineno">1011</tt>  <tt class="py-line">        <tt class="py-name">q2dens</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1012"></a><tt class="py-lineno">1012</tt>  <tt class="py-line"><tt class="py-comment">#       Determining the pooled probabilities for each phi[i]</tt> </tt>
<a name="L1013"></a><tt class="py-lineno">1013</tt>  <tt class="py-line"><tt class="py-comment">#        qtilphi = zeros(self.K)</tt> </tt>
<a name="L1014"></a><tt class="py-lineno">1014</tt>  <tt class="py-line">        <tt class="py-name">lastp</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1015"></a><tt class="py-lineno">1015</tt>  <tt class="py-line"><tt class="py-comment">#        print lastp,lastp.shape</tt> </tt>
<a name="L1016"></a><tt class="py-lineno">1016</tt>  <tt class="py-line">        <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phidens</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">lastp</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">q2dens</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">lastp</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alpha</tt> </tt>
<a name="L1017"></a><tt class="py-lineno">1017</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">qtilphi</tt><tt class="py-op">/</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1018"></a><tt class="py-lineno">1018</tt>  <tt class="py-line"> </tt>
<a name="Meld.abcRun"></a><div id="Meld.abcRun-def"><a name="L1019"></a><tt class="py-lineno">1019</tt> <a class="py-toggle" href="#" id="Meld.abcRun-toggle" onclick="return toggle('Meld.abcRun');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#abcRun">abcRun</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">fitfun</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">pool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-param">savetemp</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.abcRun-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.abcRun-expanded"><a name="L1020"></a><tt class="py-lineno">1020</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1021"></a><tt class="py-lineno">1021</tt>  <tt class="py-line"><tt class="py-docstring">        Runs the model for inference through Approximate Bayes Computation</tt> </tt>
<a name="L1022"></a><tt class="py-lineno">1022</tt>  <tt class="py-line"><tt class="py-docstring">        techniques. This method should be used as an alternative to the sir.</tt> </tt>
<a name="L1023"></a><tt class="py-lineno">1023</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1024"></a><tt class="py-lineno">1024</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L1025"></a><tt class="py-lineno">1025</tt>  <tt class="py-line"><tt class="py-docstring">             - `fitfun`: Callable which will return the goodness of fit of the model to data as a number between 0-1, with 1 meaning perfect fit</tt> </tt>
<a name="L1026"></a><tt class="py-lineno">1026</tt>  <tt class="py-line"><tt class="py-docstring">             - `t`: number of time steps to retain at the end of the of the model run for fitting purposes.</tt> </tt>
<a name="L1027"></a><tt class="py-lineno">1027</tt>  <tt class="py-line"><tt class="py-docstring">             - `data`: dict containing observed time series (lists of length t) of the state variables. This dict must have as many items the number of state variables, with labels matching variables names. Unorbserved variables must have an empty list as value.</tt> </tt>
<a name="L1028"></a><tt class="py-lineno">1028</tt>  <tt class="py-line"><tt class="py-docstring">             - `pool`: if True, Pools the user provided priors on the model's outputs, with the model induced priors.</tt> </tt>
<a name="L1029"></a><tt class="py-lineno">1029</tt>  <tt class="py-line"><tt class="py-docstring">             - `savetemp`: Should temp results be saved. Useful for long runs. Alows for resuming the simulation from last sa</tt> </tt>
<a name="L1030"></a><tt class="py-lineno">1030</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1031"></a><tt class="py-lineno">1031</tt>  <tt class="py-line">        <tt class="py-name">seed</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1032"></a><tt class="py-lineno">1032</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">fitfun</tt><tt class="py-op">:</tt> </tt>
<a name="L1033"></a><tt class="py-lineno">1033</tt>  <tt class="py-line">            <tt class="py-name">fitfun</tt> <tt class="py-op">=</tt> <tt id="link-154" class="py-name" targets="Function trunk.BIP.Bayes.Melding.basicfit()=trunk.BIP.Bayes.Melding-module.html#basicfit"><a title="trunk.BIP.Bayes.Melding.basicfit" class="py-name" href="#" onclick="return doclink('link-154', 'basicfit', 'link-154');">basicfit</a></tt> </tt>
<a name="L1034"></a><tt class="py-lineno">1034</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> </tt>
<a name="L1035"></a><tt class="py-lineno">1035</tt>  <tt class="py-line">            <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">,</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1036"></a><tt class="py-lineno">1036</tt>  <tt class="py-line"><tt class="py-comment">#       Running the model ==========================</tt> </tt>
<a name="L1037"></a><tt class="py-lineno">1037</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.runModel()=trunk.BIP.Bayes.Melding.Meld-class.html#runModel"><a title="trunk.BIP.Bayes.Melding.Meld.runModel" class="py-name" href="#" onclick="return doclink('link-155', 'runModel', 'link-155');">runModel</a></tt><tt class="py-op">(</tt><tt class="py-name">savetemp</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L1038"></a><tt class="py-lineno">1038</tt>  <tt class="py-line"> </tt>
<a name="L1039"></a><tt class="py-lineno">1039</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the K replicates\n"</tt> </tt>
<a name="L1040"></a><tt class="py-lineno">1040</tt>  <tt class="py-line">        <tt class="py-comment"># Do Log Pooling</tt> </tt>
<a name="L1041"></a><tt class="py-lineno">1041</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">pool</tt><tt class="py-op">:</tt> </tt>
<a name="L1042"></a><tt class="py-lineno">1042</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L1043"></a><tt class="py-lineno">1043</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1044"></a><tt class="py-lineno">1044</tt>  <tt class="py-line">            <tt id="link-156" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-156', 't0', 'link-72');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1045"></a><tt class="py-lineno">1045</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.logPooling()=trunk.BIP.Bayes.Melding.Meld-class.html#logPooling"><a title="trunk.BIP.Bayes.Melding.Meld.logPooling" class="py-name" href="#" onclick="return doclink('link-157', 'logPooling', 'link-157');">logPooling</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">)</tt> <tt class="py-comment">#vector with probability of each phi[i] belonging to qtilphi</tt> </tt>
<a name="L1046"></a><tt class="py-lineno">1046</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the Log Pooling (took %s seconds)\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-158" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-158', 't0', 'link-72');">t0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1047"></a><tt class="py-lineno">1047</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
<a name="L1048"></a><tt class="py-lineno">1048</tt>  <tt class="py-line">            <tt class="py-comment">#print 'max(qtilphi): ', max(qtilphi)</tt> </tt>
<a name="L1049"></a><tt class="py-lineno">1049</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L1050"></a><tt class="py-lineno">1050</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'Pooled prior on ouputs is null, please check your priors, and try again.'</tt> </tt>
<a name="L1051"></a><tt class="py-lineno">1051</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L1052"></a><tt class="py-lineno">1052</tt>  <tt class="py-line"><tt class="py-comment">#      </tt> </tt>
<a name="L1053"></a><tt class="py-lineno">1053</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Calculating weights"</tt> </tt>
<a name="L1054"></a><tt class="py-lineno">1054</tt>  <tt class="py-line">        <tt id="link-159" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-159', 'po', 'link-126');">po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1055"></a><tt class="py-lineno">1055</tt>  <tt class="py-line">        <tt class="py-name">jobs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-160" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-160', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt class="py-name">fitfun</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L1056"></a><tt class="py-lineno">1056</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">jobs</tt><tt class="py-op">]</tt> </tt>
<a name="L1057"></a><tt class="py-lineno">1057</tt>  <tt class="py-line">        <tt id="link-161" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-161', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-162" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-162', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1058"></a><tt class="py-lineno">1058</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L1059"></a><tt class="py-lineno">1059</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">w</tt> </tt>
<a name="L1060"></a><tt class="py-lineno">1060</tt>  <tt class="py-line">         </tt>
<a name="L1061"></a><tt class="py-lineno">1061</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L1062"></a><tt class="py-lineno">1062</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">qtilphi</tt> </tt>
<a name="L1063"></a><tt class="py-lineno">1063</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L1064"></a><tt class="py-lineno">1064</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L1065"></a><tt class="py-lineno">1065</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">'max(w): %s\nmin:%s\nmean(w): %s\nvar(w): %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">var</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1066"></a><tt class="py-lineno">1066</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L1067"></a><tt class="py-lineno">1067</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'Resampling weights are all zero, please check your model or data.'</tt> </tt>
<a name="L1068"></a><tt class="py-lineno">1068</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L1069"></a><tt class="py-lineno">1069</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Resampling Thetas"</tt> </tt>
<a name="L1070"></a><tt class="py-lineno">1070</tt>  <tt class="py-line">        <tt id="link-163" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-163', 't0', 'link-72');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1071"></a><tt class="py-lineno">1071</tt>  <tt class="py-line">        <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L1072"></a><tt class="py-lineno">1072</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">:</tt> <tt class="py-comment"># Extract L samples from q1theta</tt> </tt>
<a name="L1073"></a><tt class="py-lineno">1073</tt>  <tt class="py-line">            <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w and q1theta</tt> </tt>
<a name="L1074"></a><tt class="py-lineno">1074</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1075"></a><tt class="py-lineno">1075</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-comment"># retain the sample according with resampling prob.</tt> </tt>
<a name="L1076"></a><tt class="py-lineno">1076</tt>  <tt class="py-line">                <tt class="py-name">j</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L1077"></a><tt class="py-lineno">1077</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Resampling (L=%s) priors (took %s seconds)"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-164" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-164', 't0', 'link-72');">t0</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1078"></a><tt class="py-lineno">1078</tt>  <tt class="py-line"> </tt>
<a name="L1079"></a><tt class="py-lineno">1079</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L1080"></a><tt class="py-lineno">1080</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L1081"></a><tt class="py-lineno">1081</tt>  <tt class="py-line"> </tt>
<a name="Meld.imp_sample"></a><div id="Meld.imp_sample-def"><a name="L1082"></a><tt class="py-lineno">1082</tt> <a class="py-toggle" href="#" id="Meld.imp_sample-toggle" onclick="return toggle('Meld.imp_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#imp_sample">imp_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">n</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.imp_sample-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.imp_sample-expanded"><a name="L1083"></a><tt class="py-lineno">1083</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1084"></a><tt class="py-lineno">1084</tt>  <tt class="py-line"><tt class="py-docstring">        Importance sampling</tt> </tt>
<a name="L1085"></a><tt class="py-lineno">1085</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1086"></a><tt class="py-lineno">1086</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L1087"></a><tt class="py-lineno">1087</tt>  <tt class="py-line"><tt class="py-docstring">            returns a sample of size n</tt> </tt>
<a name="L1088"></a><tt class="py-lineno">1088</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1089"></a><tt class="py-lineno">1089</tt>  <tt class="py-line">        <tt class="py-comment">#sanitizing weights</tt> </tt>
<a name="L1090"></a><tt class="py-lineno">1090</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Starting importance Sampling"</tt> </tt>
<a name="L1091"></a><tt class="py-lineno">1091</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L1092"></a><tt class="py-lineno">1092</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L1093"></a><tt class="py-lineno">1093</tt>  <tt class="py-line">        <tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L1094"></a><tt class="py-lineno">1094</tt>  <tt class="py-line">        <tt class="py-name">k</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L1095"></a><tt class="py-lineno">1095</tt>  <tt class="py-line">        <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1096"></a><tt class="py-lineno">1096</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L1097"></a><tt class="py-lineno">1097</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w</tt> </tt>
<a name="L1098"></a><tt class="py-lineno">1098</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1099"></a><tt class="py-lineno">1099</tt>  <tt class="py-line">                <tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L1100"></a><tt class="py-lineno">1100</tt>  <tt class="py-line">                <tt class="py-name">j</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L1101"></a><tt class="py-lineno">1101</tt>  <tt class="py-line">                 </tt>
<a name="L1102"></a><tt class="py-lineno">1102</tt>  <tt class="py-line">            <tt class="py-name">k</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L1103"></a><tt class="py-lineno">1103</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Done imp samp."</tt> </tt>
<a name="L1104"></a><tt class="py-lineno">1104</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">smp</tt> </tt>
</div><a name="L1105"></a><tt class="py-lineno">1105</tt>  <tt class="py-line">     </tt>
<a name="Meld.mcmc_run"></a><div id="Meld.mcmc_run-def"><a name="L1106"></a><tt class="py-lineno">1106</tt> <a class="py-toggle" href="#" id="Meld.mcmc_run-toggle" onclick="return toggle('Meld.mcmc_run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#mcmc_run">mcmc_run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">likvariance</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">,</tt><tt class="py-param">burnin</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">,</tt> <tt class="py-param">nopool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">=</tt><tt class="py-string">"MH"</tt> <tt class="py-op">,</tt> <tt class="py-param">constraints</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.mcmc_run-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.mcmc_run-expanded"><a name="L1107"></a><tt class="py-lineno">1107</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1108"></a><tt class="py-lineno">1108</tt>  <tt class="py-line"><tt class="py-docstring">        MCMC based fitting</tt> </tt>
<a name="L1109"></a><tt class="py-lineno">1109</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1110"></a><tt class="py-lineno">1110</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L1111"></a><tt class="py-lineno">1111</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: observed time series on the model's output</tt> </tt>
<a name="L1112"></a><tt class="py-lineno">1112</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the observed time series</tt> </tt>
<a name="L1113"></a><tt class="py-lineno">1113</tt>  <tt class="py-line"><tt class="py-docstring">            - `likvariance`: variance of the Normal likelihood function</tt> </tt>
<a name="L1114"></a><tt class="py-lineno">1114</tt>  <tt class="py-line"><tt class="py-docstring">            - `nopool`: True if no priors on the outputs are available. Leads to faster calculations</tt> </tt>
<a name="L1115"></a><tt class="py-lineno">1115</tt>  <tt class="py-line"><tt class="py-docstring">            - `method`: Step method. defaults to Metropolis hastings</tt> </tt>
<a name="L1116"></a><tt class="py-lineno">1116</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1117"></a><tt class="py-lineno">1117</tt>  <tt class="py-line">        <tt class="py-comment">#self.phi = recarray((self.K,t),formats=['f8']*self.nphi, names = self.phi.dtype.names)</tt> </tt>
<a name="L1118"></a><tt class="py-lineno">1118</tt>  <tt class="py-line">        <tt class="py-name">ta</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-name">False</tt> </tt>
<a name="L1119"></a><tt class="py-lineno">1119</tt>  <tt class="py-line">        <tt class="py-name">tc</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-name">False</tt> </tt>
<a name="L1120"></a><tt class="py-lineno">1120</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"MH"</tt><tt class="py-op">:</tt> </tt>
<a name="L1121"></a><tt class="py-lineno">1121</tt>  <tt class="py-line">            <tt class="py-name">sampler</tt> <tt class="py-op">=</tt> <tt id="link-165" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC" class="py-name" href="#" onclick="return doclink('link-165', 'MCMC', 'link-7');">MCMC</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name" targets="Class trunk.BIP.Bayes.Samplers.MCMC.Metropolis=trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html"><a title="trunk.BIP.Bayes.Samplers.MCMC.Metropolis" class="py-name" href="#" onclick="return doclink('link-166', 'Metropolis', 'link-166');">Metropolis</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">*</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlimits</tt><tt class="py-op">,</tt> <tt id="link-167" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-167', 'like', 'link-3');">like</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name" targets="Function trunk.BIP.Bayes.like.Normal()=trunk.BIP.Bayes.like-module.html#Normal"><a title="trunk.BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-168', 'Normal', 'link-168');">Normal</a></tt><tt class="py-op">,</tt> <tt class="py-name">likvariance</tt><tt class="py-op">,</tt> <tt class="py-name">burnin</tt><tt class="py-op">,</tt> <tt id="link-169" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#trace_acceptance"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-169', 'trace_acceptance', 'link-169');">trace_acceptance</a></tt><tt class="py-op">=</tt><tt class="py-name">ta</tt><tt class="py-op">,</tt>  <tt id="link-170" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#trace_convergence"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence" class="py-name" href="#" onclick="return doclink('link-170', 'trace_convergence', 'link-170');">trace_convergence</a></tt><tt class="py-op">=</tt><tt class="py-name">tc</tt><tt class="py-op">,</tt> <tt class="py-name">nchains</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">,</tt> <tt class="py-name">constraints</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1122"></a><tt class="py-lineno">1122</tt>  <tt class="py-line">            <tt class="py-name">sampler</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-171', 'step', 'link-127');">step</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1123"></a><tt class="py-lineno">1123</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">sampler</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> </tt>
<a name="L1124"></a><tt class="py-lineno">1124</tt>  <tt class="py-line">            <tt class="py-comment">#self.mh(self.K,t,data,like.Normal,likvariance,burnin)</tt> </tt>
<a name="L1125"></a><tt class="py-lineno">1125</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">'dream'</tt><tt class="py-op">:</tt> </tt>
<a name="L1126"></a><tt class="py-lineno">1126</tt>  <tt class="py-line">            <tt class="py-name">sampler</tt> <tt class="py-op">=</tt> <tt id="link-172" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC" class="py-name" href="#" onclick="return doclink('link-172', 'MCMC', 'link-7');">MCMC</a></tt><tt class="py-op">.</tt><tt id="link-173" class="py-name" targets="Class trunk.BIP.Bayes.Samplers.MCMC.Dream=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream" class="py-name" href="#" onclick="return doclink('link-173', 'Dream', 'link-173');">Dream</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">*</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tlimits</tt><tt class="py-op">,</tt> <tt id="link-174" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-174', 'like', 'link-3');">like</a></tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="trunk.BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-175', 'Normal', 'link-168');">Normal</a></tt><tt class="py-op">,</tt> <tt class="py-name">likvariance</tt><tt class="py-op">,</tt> <tt class="py-name">burnin</tt><tt class="py-op">,</tt> <tt id="link-176" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-176', 'trace_acceptance', 'link-169');">trace_acceptance</a></tt><tt class="py-op">=</tt><tt class="py-name">ta</tt><tt class="py-op">,</tt>  <tt id="link-177" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence" class="py-name" href="#" onclick="return doclink('link-177', 'trace_convergence', 'link-170');">trace_convergence</a></tt><tt class="py-op">=</tt><tt class="py-name">tc</tt><tt class="py-op">,</tt> <tt class="py-name">nchains</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">,</tt> <tt class="py-name">constraints</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1127"></a><tt class="py-lineno">1127</tt>  <tt class="py-line">            <tt class="py-name">sampler</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-178', 'step', 'link-127');">step</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1128"></a><tt class="py-lineno">1128</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">sampler</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> </tt>
<a name="L1129"></a><tt class="py-lineno">1129</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1130"></a><tt class="py-lineno">1130</tt>  <tt class="py-line">            <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid MCMC method!\nTry 'MH'."</tt><tt class="py-op">)</tt> </tt>
<a name="L1131"></a><tt class="py-lineno">1131</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L1132"></a><tt class="py-lineno">1132</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L1133"></a><tt class="py-lineno">1133</tt>  <tt class="py-line">         </tt>
<a name="Meld._output_loglike"></a><div id="Meld._output_loglike-def"><a name="L1134"></a><tt class="py-lineno">1134</tt> <a class="py-toggle" href="#" id="Meld._output_loglike-toggle" onclick="return toggle('Meld._output_loglike');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#_output_loglike">_output_loglike</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prop</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">likfun</tt><tt class="py-op">=</tt><tt id="link-179" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-179', 'like', 'link-3');">like</a></tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="trunk.BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-180', 'Normal', 'link-168');">Normal</a></tt><tt class="py-op">,</tt><tt class="py-param">likvar</tt><tt class="py-op">=</tt><tt class="py-number">1e-1</tt><tt class="py-op">,</tt> <tt class="py-param">po</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld._output_loglike-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld._output_loglike-expanded"><a name="L1135"></a><tt class="py-lineno">1135</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1136"></a><tt class="py-lineno">1136</tt>  <tt class="py-line"><tt class="py-docstring">        Returns the log-likelihood of a simulated series</tt> </tt>
<a name="L1137"></a><tt class="py-lineno">1137</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1138"></a><tt class="py-lineno">1138</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L1139"></a><tt class="py-lineno">1139</tt>  <tt class="py-line"><tt class="py-docstring">            - `prop`: Proposed output</tt> </tt>
<a name="L1140"></a><tt class="py-lineno">1140</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Data against which proposal will be measured</tt> </tt>
<a name="L1141"></a><tt class="py-lineno">1141</tt>  <tt class="py-line"><tt class="py-docstring">            - `likfun`: Likelihood function</tt> </tt>
<a name="L1142"></a><tt class="py-lineno">1142</tt>  <tt class="py-line"><tt class="py-docstring">            - `likvar`: Variance of the likelihood function</tt> </tt>
<a name="L1143"></a><tt class="py-lineno">1143</tt>  <tt class="py-line"><tt class="py-docstring">            - `po`: Pool of processes for parallel execution</tt> </tt>
<a name="L1144"></a><tt class="py-lineno">1144</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1145"></a><tt class="py-lineno">1145</tt>  <tt class="py-line"><tt class="py-docstring">        :Types:</tt> </tt>
<a name="L1146"></a><tt class="py-lineno">1146</tt>  <tt class="py-line"><tt class="py-docstring">            - `prop`: array of shape (t,nphi) with series as columns.</tt> </tt>
<a name="L1147"></a><tt class="py-lineno">1147</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Dictionary with keys being the names (as in phinames) of observed variables</tt> </tt>
<a name="L1148"></a><tt class="py-lineno">1148</tt>  <tt class="py-line"><tt class="py-docstring">            - `likfun`: Log likelihood function object</tt> </tt>
<a name="L1149"></a><tt class="py-lineno">1149</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1150"></a><tt class="py-lineno">1150</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">prop</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">recarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1151"></a><tt class="py-lineno">1151</tt>  <tt class="py-line">            <tt class="py-name">prop</tt><tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">prop</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1152"></a><tt class="py-lineno">1152</tt>  <tt class="py-line">        <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">prop</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-comment">#1 if model's output is a scalar, larger if it is a time series (or a set of them)</tt> </tt>
<a name="L1153"></a><tt class="py-lineno">1153</tt>  <tt class="py-line">        <tt class="py-name">lik</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L1154"></a><tt class="py-lineno">1154</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#loop on series</tt> </tt>
<a name="L1155"></a><tt class="py-lineno">1155</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">:</tt> </tt>
<a name="L1156"></a><tt class="py-lineno">1156</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt><tt class="py-comment">#Only calculate liks of series for which we have data</tt> </tt>
<a name="L1157"></a><tt class="py-lineno">1157</tt>  <tt class="py-line">            <tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1158"></a><tt class="py-lineno">1158</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-comment">#in case of more than one dataset</tt> </tt>
<a name="L1159"></a><tt class="py-lineno">1159</tt>  <tt class="py-line">                <tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt id="link-181" class="py-name" targets="Function trunk.BIP.Bayes.Melding.clearNaN()=trunk.BIP.Bayes.Melding-module.html#clearNaN"><a title="trunk.BIP.Bayes.Melding.clearNaN" class="py-name" href="#" onclick="return doclink('link-181', 'clearNaN', 'link-181');">clearNaN</a></tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1160"></a><tt class="py-lineno">1160</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-182" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-182', 'po', 'link-126');">po</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt><tt class="py-comment"># Parallel version</tt> </tt>
<a name="L1161"></a><tt class="py-lineno">1161</tt>  <tt class="py-line">                <tt class="py-name">liks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-183" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-183', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt class="py-name">likfun</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">prop</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">likvar</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L1162"></a><tt class="py-lineno">1162</tt>  <tt class="py-line">                <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-name">nansum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">liks</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1163"></a><tt class="py-lineno">1163</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1164"></a><tt class="py-lineno">1164</tt>  <tt class="py-line">                <tt class="py-name">liks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">likfun</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">prop</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">likvar</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">]</tt> </tt>
<a name="L1165"></a><tt class="py-lineno">1165</tt>  <tt class="py-line">                <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-name">nansum</tt><tt class="py-op">(</tt><tt class="py-name">liks</tt><tt class="py-op">)</tt> </tt>
<a name="L1166"></a><tt class="py-lineno">1166</tt>  <tt class="py-line"><tt class="py-comment">#                if isnan(lik):</tt> </tt>
<a name="L1167"></a><tt class="py-lineno">1167</tt>  <tt class="py-line"><tt class="py-comment">#                    pdb.set_trace()</tt> </tt>
<a name="L1168"></a><tt class="py-lineno">1168</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">lik</tt> </tt>
</div><a name="L1169"></a><tt class="py-lineno">1169</tt>  <tt class="py-line">     </tt>
<a name="Meld.sir"></a><div id="Meld.sir-def"><a name="L1170"></a><tt class="py-lineno">1170</tt> <a class="py-toggle" href="#" id="Meld.sir-toggle" onclick="return toggle('Meld.sir');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#sir">sir</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">variance</tt><tt class="py-op">=</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt> <tt class="py-param">pool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-param">savetemp</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.sir-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.sir-expanded"><a name="L1171"></a><tt class="py-lineno">1171</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1172"></a><tt class="py-lineno">1172</tt>  <tt class="py-line"><tt class="py-docstring">        Run the model output through the Sampling-Importance-Resampling algorithm.</tt> </tt>
<a name="L1173"></a><tt class="py-lineno">1173</tt>  <tt class="py-line"><tt class="py-docstring">        Returns 1 if successful or 0 if not.</tt> </tt>
<a name="L1174"></a><tt class="py-lineno">1174</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1175"></a><tt class="py-lineno">1175</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L1176"></a><tt class="py-lineno">1176</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: observed time series on the model's output</tt> </tt>
<a name="L1177"></a><tt class="py-lineno">1177</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the observed time series</tt> </tt>
<a name="L1178"></a><tt class="py-lineno">1178</tt>  <tt class="py-line"><tt class="py-docstring">            - `variance`: variance of the Normal likelihood function</tt> </tt>
<a name="L1179"></a><tt class="py-lineno">1179</tt>  <tt class="py-line"><tt class="py-docstring">            - `pool`: False if no priors on the outputs are available. Leads to faster calculations</tt> </tt>
<a name="L1180"></a><tt class="py-lineno">1180</tt>  <tt class="py-line"><tt class="py-docstring">            - `savetemp`: Boolean. create a temp file?</tt> </tt>
<a name="L1181"></a><tt class="py-lineno">1181</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1182"></a><tt class="py-lineno">1182</tt>  <tt class="py-line">        <tt class="py-name">seed</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1183"></a><tt class="py-lineno">1183</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.runModel" class="py-name" href="#" onclick="return doclink('link-184', 'runModel', 'link-155');">runModel</a></tt><tt class="py-op">(</tt><tt class="py-name">savetemp</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L1184"></a><tt class="py-lineno">1184</tt>  <tt class="py-line">        <tt class="py-comment"># Do Log Pooling</tt> </tt>
<a name="L1185"></a><tt class="py-lineno">1185</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">pool</tt><tt class="py-op">:</tt> </tt>
<a name="L1186"></a><tt class="py-lineno">1186</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L1187"></a><tt class="py-lineno">1187</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1188"></a><tt class="py-lineno">1188</tt>  <tt class="py-line">            <tt id="link-185" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-185', 't0', 'link-72');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1189"></a><tt class="py-lineno">1189</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.logPooling" class="py-name" href="#" onclick="return doclink('link-186', 'logPooling', 'link-157');">logPooling</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">)</tt> <tt class="py-comment">#vector with probability of each phi[i] belonging to qtilphi</tt> </tt>
<a name="L1190"></a><tt class="py-lineno">1190</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the Log Pooling (took %s seconds)\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-187" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-187', 't0', 'link-72');">t0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1191"></a><tt class="py-lineno">1191</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
<a name="L1192"></a><tt class="py-lineno">1192</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'max(qtilphi): '</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
<a name="L1193"></a><tt class="py-lineno">1193</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L1194"></a><tt class="py-lineno">1194</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'Pooled prior on ouputs is null, please check your priors, and try again.'</tt> </tt>
<a name="L1195"></a><tt class="py-lineno">1195</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L1196"></a><tt class="py-lineno">1196</tt>  <tt class="py-line"> </tt>
<a name="L1197"></a><tt class="py-lineno">1197</tt>  <tt class="py-line"><tt class="py-comment">#       Calculating the likelihood of each phi[i] considering the observed data</tt> </tt>
<a name="L1198"></a><tt class="py-lineno">1198</tt>  <tt class="py-line"><tt class="py-comment">#        lik =self._output_loglike()</tt> </tt>
<a name="L1199"></a><tt class="py-lineno">1199</tt>  <tt class="py-line">        <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L1200"></a><tt class="py-lineno">1200</tt>  <tt class="py-line">        <tt id="link-188" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-188', 't0', 'link-72');">t0</a></tt><tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1201"></a><tt class="py-lineno">1201</tt>  <tt class="py-line">        <tt id="link-189" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-189', 'po', 'link-126');">po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1202"></a><tt class="py-lineno">1202</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1203"></a><tt class="py-lineno">1203</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L1204"></a><tt class="py-lineno">1204</tt>  <tt class="py-line">            <tt class="py-name">l</tt> <tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld._output_loglike()=trunk.BIP.Bayes.Melding.Meld-class.html#_output_loglike"><a title="trunk.BIP.Bayes.Melding.Meld._output_loglike" class="py-name" href="#" onclick="return doclink('link-190', '_output_loglike', 'link-190');">_output_loglike</a></tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">,</tt>  <tt class="py-name">likvar</tt><tt class="py-op">=</tt><tt class="py-name">variance</tt><tt class="py-op">)</tt> </tt>
<a name="L1205"></a><tt class="py-lineno">1205</tt>  <tt class="py-line"><tt class="py-comment">#            for n in data.keys():</tt> </tt>
<a name="L1206"></a><tt class="py-lineno">1206</tt>  <tt class="py-line"><tt class="py-comment">#                if isinstance(data[n],list) and data[n] == []: </tt> </tt>
<a name="L1207"></a><tt class="py-lineno">1207</tt>  <tt class="py-line"><tt class="py-comment">#                    continue #no observations for this variable</tt> </tt>
<a name="L1208"></a><tt class="py-lineno">1208</tt>  <tt class="py-line"><tt class="py-comment">#                elif isinstance(data[n],numpy.ndarray) and (not data[n].any()):</tt> </tt>
<a name="L1209"></a><tt class="py-lineno">1209</tt>  <tt class="py-line"><tt class="py-comment">#                    continue #no observations for this variable</tt> </tt>
<a name="L1210"></a><tt class="py-lineno">1210</tt>  <tt class="py-line"><tt class="py-comment">#                p = phi[n]</tt> </tt>
<a name="L1211"></a><tt class="py-lineno">1211</tt>  <tt class="py-line"><tt class="py-comment">#                lik =self._output_loglike()</tt> </tt>
<a name="L1212"></a><tt class="py-lineno">1212</tt>  <tt class="py-line"><tt class="py-comment">#                liklist=[po.apply_async(like.Normal,(data[n][m], j, 1./variance)) for m,j in enumerate(p[i])]</tt> </tt>
<a name="L1213"></a><tt class="py-lineno">1213</tt>  <tt class="py-line"><tt class="py-comment">#                l=sum([p.get() for p in liklist])</tt> </tt>
<a name="L1214"></a><tt class="py-lineno">1214</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">/</tt><tt class="py-number">10.</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L1215"></a><tt class="py-lineno">1215</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"Likelihood calculation progress: %s of %s done."</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L1216"></a><tt class="py-lineno">1216</tt>  <tt class="py-line">            <tt class="py-name">lik</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">l</tt> </tt>
<a name="L1217"></a><tt class="py-lineno">1217</tt>  <tt class="py-line">        <tt id="link-191" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-191', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1218"></a><tt class="py-lineno">1218</tt>  <tt class="py-line">        <tt id="link-192" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-192', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1219"></a><tt class="py-lineno">1219</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="trunk.BIP.SDE.gillespie.viz" class="py-name" href="#" onclick="return doclink('link-193', 'viz', 'link-122');">viz</a></tt><tt class="py-op">:</tt> </tt>
<a name="L1220"></a><tt class="py-lineno">1220</tt>  <tt class="py-line">            <tt id="link-194" class="py-name"><a title="trunk.BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-194', 'dtplot', 'link-16');">dtplot</a></tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-195', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-196" class="py-name"><a title="trunk.BIP.Bayes.Melding.phiplot" class="py-name" href="#" onclick="return doclink('link-196', 'phiplot', 'link-18');">phiplot</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-197', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-198" class="py-name"><a title="trunk.BIP.Bayes.Melding.thplot" class="py-name" href="#" onclick="return doclink('link-198', 'thplot', 'link-20');">thplot</a></tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-199', 'clearFig', 'link-104');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1221"></a><tt class="py-lineno">1221</tt>  <tt class="py-line">            <tt id="link-200" class="py-name"><a title="trunk.BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-200', 'dtplot', 'link-16');">dtplot</a></tt><tt class="py-op">.</tt><tt class="py-name">gp</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'observed'</tt><tt class="py-op">)</tt> </tt>
<a name="L1222"></a><tt class="py-lineno">1222</tt>  <tt class="py-line">            <tt id="link-201" class="py-name"><a title="trunk.BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-201', 'dtplot', 'link-16');">dtplot</a></tt><tt class="py-op">.</tt><tt class="py-name">gp</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'simulated'</tt><tt class="py-op">)</tt> </tt>
<a name="L1223"></a><tt class="py-lineno">1223</tt>  <tt class="py-line">            <tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">;</tt><tt class="py-name">sim</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1224"></a><tt class="py-lineno">1224</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1225"></a><tt class="py-lineno">1225</tt>  <tt class="py-line">                <tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1226"></a><tt class="py-lineno">1226</tt>  <tt class="py-line">                <tt class="py-name">sim</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1227"></a><tt class="py-lineno">1227</tt>  <tt class="py-line">            <tt id="link-202" class="py-name"><a title="trunk.BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-202', 'dtplot', 'link-16');">dtplot</a></tt><tt class="py-op">.</tt><tt id="link-203" class="py-name" targets="Method trunk.BIP.Viz.realtime.RTplot.scatter()=trunk.BIP.Viz.realtime.RTplot-class.html#scatter"><a title="trunk.BIP.Viz.realtime.RTplot.scatter" class="py-name" href="#" onclick="return doclink('link-203', 'scatter', 'link-203');">scatter</a></tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">sim</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'fit'</tt><tt class="py-op">)</tt> </tt>
<a name="L1228"></a><tt class="py-lineno">1228</tt>  <tt class="py-line">            <tt id="link-204" class="py-name"><a title="trunk.BIP.Bayes.Melding.phiplot" class="py-name" href="#" onclick="return doclink('link-204', 'phiplot', 'link-18');">phiplot</a></tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.plotlines
trunk.BIP.Viz.realtime.RTpyplot.plotlines" class="py-name" href="#" onclick="return doclink('link-205', 'plotlines', 'link-37');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">sim</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Model Output'</tt><tt class="py-op">)</tt> </tt>
<a name="L1229"></a><tt class="py-lineno">1229</tt>  <tt class="py-line">            <tt id="link-206" class="py-name"><a title="trunk.BIP.Bayes.Melding.thplot" class="py-name" href="#" onclick="return doclink('link-206', 'thplot', 'link-20');">thplot</a></tt><tt class="py-op">.</tt><tt id="link-207" class="py-name" targets="Method trunk.BIP.Viz.realtime.RTplot.plothist()=trunk.BIP.Viz.realtime.RTplot-class.html#plothist"><a title="trunk.BIP.Viz.realtime.RTplot.plothist" class="py-name" href="#" onclick="return doclink('link-207', 'plothist', 'link-207');">plothist</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Input parameters'</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L1230"></a><tt class="py-lineno">1230</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Calculating Likelihoods (took %s seconds)"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-208" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-208', 't0', 'link-72');">t0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1231"></a><tt class="py-lineno">1231</tt>  <tt class="py-line">        <tt class="py-name">lr</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1232"></a><tt class="py-lineno">1232</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; Likelihood (min,mean,max,sum): '</tt><tt class="py-op">,</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L1233"></a><tt class="py-lineno">1233</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Likelihood ratio of best run/worst run: %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">lr</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L1234"></a><tt class="py-lineno">1234</tt>  <tt class="py-line"><tt class="py-comment">#        Calculating the weights</tt> </tt>
<a name="L1235"></a><tt class="py-lineno">1235</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">*</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L1236"></a><tt class="py-lineno">1236</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">/</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1237"></a><tt class="py-lineno">1237</tt>  <tt class="py-line"> </tt>
<a name="L1238"></a><tt class="py-lineno">1238</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L1239"></a><tt class="py-lineno">1239</tt>  <tt class="py-line">            <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L1240"></a><tt class="py-lineno">1240</tt>  <tt class="py-line">            <tt id="link-209" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-209', 't0', 'link-72');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1241"></a><tt class="py-lineno">1241</tt>  <tt class="py-line">            <tt class="py-name">maxw</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">minw</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-comment">#keep track of goodness of fit of phi</tt> </tt>
<a name="L1242"></a><tt class="py-lineno">1242</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">:</tt> <tt class="py-comment"># Extract L samples from q1theta</tt> </tt>
<a name="L1243"></a><tt class="py-lineno">1243</tt>  <tt class="py-line">                <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w and q1theta</tt> </tt>
<a name="L1244"></a><tt class="py-lineno">1244</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1245"></a><tt class="py-lineno">1245</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-comment"># retain the sample according with resampling prob.</tt> </tt>
<a name="L1246"></a><tt class="py-lineno">1246</tt>  <tt class="py-line">                    <tt class="py-name">maxw</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">maxw</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1247"></a><tt class="py-lineno">1247</tt>  <tt class="py-line">                    <tt class="py-name">minw</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">minw</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1248"></a><tt class="py-lineno">1248</tt>  <tt class="py-line">                    <tt class="py-name">j</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L1249"></a><tt class="py-lineno">1249</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">j</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L1250"></a><tt class="py-lineno">1250</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-string">"of %s"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt> </tt>
<a name="L1251"></a><tt class="py-lineno">1251</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L1252"></a><tt class="py-lineno">1252</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Resampling (L=%s) priors (took %s seconds)"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-210" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-210', 't0', 'link-72');">t0</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1253"></a><tt class="py-lineno">1253</tt>  <tt class="py-line">            <tt class="py-name">wr</tt> <tt class="py-op">=</tt> <tt class="py-name">maxw</tt><tt class="py-op">/</tt><tt class="py-name">minw</tt> </tt>
<a name="L1254"></a><tt class="py-lineno">1254</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Likelihood ratio of best/worst retained runs: %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">wr</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L1255"></a><tt class="py-lineno">1255</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">wr</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L1256"></a><tt class="py-lineno">1256</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Flat likelihood, trying again..."</tt> </tt>
<a name="L1257"></a><tt class="py-lineno">1257</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L1258"></a><tt class="py-lineno">1258</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Improvement: %s percent"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-number">100</tt><tt class="py-op">-</tt><tt class="py-number">100</tt><tt class="py-op">*</tt><tt class="py-name">wr</tt><tt class="py-op">/</tt><tt class="py-name">lr</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L1259"></a><tt class="py-lineno">1259</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1260"></a><tt class="py-lineno">1260</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'Resampling weights are all zero, please check your model or data, and try again.\n'</tt> </tt>
<a name="L1261"></a><tt class="py-lineno">1261</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; Likelihood (min,mean,max): '</tt><tt class="py-op">,</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L1262"></a><tt class="py-lineno">1262</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; RMS deviation of outputs: %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt id="link-211" class="py-name"><a title="trunk.BIP.Bayes.Melding.basicfit" class="py-name" href="#" onclick="return doclink('link-211', 'basicfit', 'link-154');">basicfit</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L1263"></a><tt class="py-lineno">1263</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L1264"></a><tt class="py-lineno">1264</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L1265"></a><tt class="py-lineno">1265</tt>  <tt class="py-line"> </tt>
<a name="L1266"></a><tt class="py-lineno">1266</tt>  <tt class="py-line">         </tt>
<a name="Meld.runModel"></a><div id="Meld.runModel-def"><a name="L1267"></a><tt class="py-lineno">1267</tt> <a class="py-toggle" href="#" id="Meld.runModel-toggle" onclick="return toggle('Meld.runModel');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding.Meld-class.html#runModel">runModel</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">savetemp</tt><tt class="py-op">,</tt><tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">k</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.runModel-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Meld.runModel-expanded"><a name="L1268"></a><tt class="py-lineno">1268</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L1269"></a><tt class="py-lineno">1269</tt>  <tt class="py-line"><tt class="py-docstring">        Handles running the model k times keeping a temporary savefile for</tt> </tt>
<a name="L1270"></a><tt class="py-lineno">1270</tt>  <tt class="py-line"><tt class="py-docstring">        resuming calculation in case of interruption.</tt> </tt>
<a name="L1271"></a><tt class="py-lineno">1271</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1272"></a><tt class="py-lineno">1272</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L1273"></a><tt class="py-lineno">1273</tt>  <tt class="py-line"><tt class="py-docstring">            - `savetemp`: Boolean. create a temp file?</tt> </tt>
<a name="L1274"></a><tt class="py-lineno">1274</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: number of time steps</tt> </tt>
<a name="L1275"></a><tt class="py-lineno">1275</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1276"></a><tt class="py-lineno">1276</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L1277"></a><tt class="py-lineno">1277</tt>  <tt class="py-line"><tt class="py-docstring">            - self.phi: a record array of shape (k,t) with the results.</tt> </tt>
<a name="L1278"></a><tt class="py-lineno">1278</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L1279"></a><tt class="py-lineno">1279</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> </tt>
<a name="L1280"></a><tt class="py-lineno">1280</tt>  <tt class="py-line">            <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">,</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1281"></a><tt class="py-lineno">1281</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">k</tt><tt class="py-op">:</tt> </tt>
<a name="L1282"></a><tt class="py-lineno">1282</tt>  <tt class="py-line">            <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt> </tt>
<a name="L1283"></a><tt class="py-lineno">1283</tt>  <tt class="py-line"><tt class="py-comment">#       Running the model ==========================</tt> </tt>
<a name="L1284"></a><tt class="py-lineno">1284</tt>  <tt class="py-line">         </tt>
<a name="L1285"></a><tt class="py-lineno">1285</tt>  <tt class="py-line">                 </tt>
<a name="L1286"></a><tt class="py-lineno">1286</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1287"></a><tt class="py-lineno">1287</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1288"></a><tt class="py-lineno">1288</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1289"></a><tt class="py-lineno">1289</tt>  <tt class="py-line">            <tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L1290"></a><tt class="py-lineno">1290</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L1291"></a><tt class="py-lineno">1291</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">cb</tt><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1292"></a><tt class="py-lineno">1292</tt>  <tt class="py-line">            <tt class="py-docstring">'''</tt> </tt>
<a name="L1293"></a><tt class="py-lineno">1293</tt>  <tt class="py-line"><tt class="py-docstring">            callback function for the asynchronous model runs</tt> </tt>
<a name="L1294"></a><tt class="py-lineno">1294</tt>  <tt class="py-line"><tt class="py-docstring">            '''</tt> </tt>
<a name="L1295"></a><tt class="py-lineno">1295</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L1296"></a><tt class="py-lineno">1296</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt id="link-212" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-212', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-213" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-213', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L1297"></a><tt class="py-lineno">1297</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1298"></a><tt class="py-lineno">1298</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt id="link-214" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-214', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt id="link-215" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-215', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-comment"># #phi is the last t points in the simulation</tt> </tt>
</div><a name="L1299"></a><tt class="py-lineno">1299</tt>  <tt class="py-line"> </tt>
<a name="L1300"></a><tt class="py-lineno">1300</tt>  <tt class="py-line">        <tt id="link-216" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-216', 'po', 'link-126');">po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1301"></a><tt class="py-lineno">1301</tt>  <tt class="py-line">        <tt id="link-217" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-217', 't0', 'link-72');">t0</a></tt><tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1302"></a><tt class="py-lineno">1302</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">k</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1303"></a><tt class="py-lineno">1303</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L1304"></a><tt class="py-lineno">1304</tt>  <tt class="py-line">            <tt id="link-218" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-218', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt id="link-219" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-219', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-220" class="py-name"><a title="trunk.BIP.Bayes.Melding.enumRun" class="py-name" href="#" onclick="return doclink('link-220', 'enumRun', 'link-147');">enumRun</a></tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-221', 'model', 'link-22');">model</a></tt><tt class="py-op">,</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">callback</tt><tt class="py-op">=</tt><tt class="py-name">cb</tt><tt class="py-op">)</tt> </tt>
<a name="L1305"></a><tt class="py-lineno">1305</tt>  <tt class="py-line"><tt class="py-comment">#            r = po.apply_async(self.model,theta)</tt> </tt>
<a name="L1306"></a><tt class="py-lineno">1306</tt>  <tt class="py-line"><tt class="py-comment">#            if t == 1:</tt> </tt>
<a name="L1307"></a><tt class="py-lineno">1307</tt>  <tt class="py-line"><tt class="py-comment">#                phi[i] = (r.get()[-1],)</tt> </tt>
<a name="L1308"></a><tt class="py-lineno">1308</tt>  <tt class="py-line"><tt class="py-comment">#            else:</tt> </tt>
<a name="L1309"></a><tt class="py-lineno">1309</tt>  <tt class="py-line"><tt class="py-comment">#                phi[i] = [tuple(l) for l in r.get()[-t:]]# #phi is the last t points in the simulation</tt> </tt>
<a name="L1310"></a><tt class="py-lineno">1310</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L1311"></a><tt class="py-lineno">1311</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; K = %s"</tt><tt class="py-op">%</tt><tt class="py-name">i</tt> </tt>
<a name="L1312"></a><tt class="py-lineno">1312</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> </tt>
<a name="L1313"></a><tt class="py-lineno">1313</tt>  <tt class="py-line">                    <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1314"></a><tt class="py-lineno">1314</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> <tt class="py-comment">#If all replicates are done, clear temporary save files.</tt> </tt>
<a name="L1315"></a><tt class="py-lineno">1315</tt>  <tt class="py-line">            <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">unlink</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">)</tt> </tt>
<a name="L1316"></a><tt class="py-lineno">1316</tt>  <tt class="py-line">            <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">unlink</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">)</tt> </tt>
<a name="L1317"></a><tt class="py-lineno">1317</tt>  <tt class="py-line">        <tt id="link-222" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-222', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1318"></a><tt class="py-lineno">1318</tt>  <tt class="py-line">        <tt id="link-223" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-223', 'po', 'link-126');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1319"></a><tt class="py-lineno">1319</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the K (%s) replicates (took %s seconds)\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-224" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-224', 't0', 'link-72');">t0</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1320"></a><tt class="py-lineno">1320</tt>  <tt class="py-line">         </tt>
<a name="L1321"></a><tt class="py-lineno">1321</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> </tt>
</div></div><a name="L1322"></a><tt class="py-lineno">1322</tt>  <tt class="py-line"> </tt>
<a name="basicfit"></a><div id="basicfit-def"><a name="L1323"></a><tt class="py-lineno">1323</tt> <a class="py-toggle" href="#" id="basicfit-toggle" onclick="return toggle('basicfit');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#basicfit">basicfit</a><tt class="py-op">(</tt><tt class="py-param">s1</tt><tt class="py-op">,</tt><tt class="py-param">s2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="basicfit-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="basicfit-expanded"><a name="L1324"></a><tt class="py-lineno">1324</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L1325"></a><tt class="py-lineno">1325</tt>  <tt class="py-line"><tt class="py-docstring">    Calculates a basic fitness calculation between a model-</tt> </tt>
<a name="L1326"></a><tt class="py-lineno">1326</tt>  <tt class="py-line"><tt class="py-docstring">    generated time series and a observed time series.</tt> </tt>
<a name="L1327"></a><tt class="py-lineno">1327</tt>  <tt class="py-line"><tt class="py-docstring">    it uses a Mean square error.</tt> </tt>
<a name="L1328"></a><tt class="py-lineno">1328</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1329"></a><tt class="py-lineno">1329</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L1330"></a><tt class="py-lineno">1330</tt>  <tt class="py-line"><tt class="py-docstring">        - `s1`: model-generated time series. record array.</tt> </tt>
<a name="L1331"></a><tt class="py-lineno">1331</tt>  <tt class="py-line"><tt class="py-docstring">        - `s2`: observed time series. dictionary with keys matching names of s1</tt> </tt>
<a name="L1332"></a><tt class="py-lineno">1332</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1333"></a><tt class="py-lineno">1333</tt>  <tt class="py-line"><tt class="py-docstring">    :Return:</tt> </tt>
<a name="L1334"></a><tt class="py-lineno">1334</tt>  <tt class="py-line"><tt class="py-docstring">        Root mean square deviation between &#180;s1&#180; and &#180;s2&#180;.</tt> </tt>
<a name="L1335"></a><tt class="py-lineno">1335</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L1336"></a><tt class="py-lineno">1336</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">recarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1337"></a><tt class="py-lineno">1337</tt>  <tt class="py-line"><tt class="py-comment">#        print "==&gt; is recarray!"</tt> </tt>
<a name="L1338"></a><tt class="py-lineno">1338</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt> </tt>
<a name="L1339"></a><tt class="py-lineno">1339</tt>  <tt class="py-line">        <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1340"></a><tt class="py-lineno">1340</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1341"></a><tt class="py-lineno">1341</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">k</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s1</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L1342"></a><tt class="py-lineno">1342</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1343"></a><tt class="py-lineno">1343</tt>  <tt class="py-line">            <tt class="py-name">ls1</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment">#handles the cases where data is slightly longer that simulated series.</tt> </tt>
<a name="L1344"></a><tt class="py-lineno">1344</tt>  <tt class="py-line"><tt class="py-comment">#                print s2[k]</tt> </tt>
<a name="L1345"></a><tt class="py-lineno">1345</tt>  <tt class="py-line"><tt class="py-comment">#                try:</tt> </tt>
<a name="L1346"></a><tt class="py-lineno">1346</tt>  <tt class="py-line"><tt class="py-comment">#                pdb.set_trace()</tt> </tt>
<a name="L1347"></a><tt class="py-lineno">1347</tt>  <tt class="py-line"> </tt>
<a name="L1348"></a><tt class="py-lineno">1348</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L1349"></a><tt class="py-lineno">1349</tt>  <tt class="py-line">                <tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-225" class="py-name"><a title="trunk.BIP.Bayes.Melding.clearNaN" class="py-name" href="#" onclick="return doclink('link-225', 'clearNaN', 'link-181');">clearNaN</a></tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-comment">#nanmean(s2[k], axis=1)</tt> </tt>
<a name="L1350"></a><tt class="py-lineno">1350</tt>  <tt class="py-line">            <tt class="py-name">dif</tt> <tt class="py-op">=</tt> <tt class="py-name">s1</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">ls1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L1351"></a><tt class="py-lineno">1351</tt>  <tt class="py-line">             </tt>
<a name="L1352"></a><tt class="py-lineno">1352</tt>  <tt class="py-line">            <tt class="py-name">dif</tt><tt class="py-op">[</tt><tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L1353"></a><tt class="py-lineno">1353</tt>  <tt class="py-line">            <tt id="link-226" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-226', 'e', 'link-43');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">nanmean</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L1354"></a><tt class="py-lineno">1354</tt>  <tt class="py-line"><tt class="py-comment">#                except TypeError:</tt> </tt>
<a name="L1355"></a><tt class="py-lineno">1355</tt>  <tt class="py-line"><tt class="py-comment">#                    print s1[k], s2[k]</tt> </tt>
<a name="L1356"></a><tt class="py-lineno">1356</tt>  <tt class="py-line"> </tt>
<a name="L1357"></a><tt class="py-lineno">1357</tt>  <tt class="py-line">            <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-227" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-227', 'e', 'link-43');">e</a></tt><tt class="py-op">)</tt>  </tt>
<a name="L1358"></a><tt class="py-lineno">1358</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1359"></a><tt class="py-lineno">1359</tt>  <tt class="py-line"><tt class="py-comment">#        print "==&gt; is List!"</tt> </tt>
<a name="L1360"></a><tt class="py-lineno">1360</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt> </tt>
<a name="L1361"></a><tt class="py-lineno">1361</tt>  <tt class="py-line">        <tt class="py-name">s1</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L1362"></a><tt class="py-lineno">1362</tt>  <tt class="py-line">        <tt class="py-name">s2</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L1363"></a><tt class="py-lineno">1363</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L1364"></a><tt class="py-lineno">1364</tt>  <tt class="py-line">            <tt class="py-name">s2</tt> <tt class="py-op">=</tt> <tt id="link-228" class="py-name"><a title="trunk.BIP.Bayes.Melding.clearNaN" class="py-name" href="#" onclick="return doclink('link-228', 'clearNaN', 'link-181');">clearNaN</a></tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1365"></a><tt class="py-lineno">1365</tt>  <tt class="py-line">         </tt>
<a name="L1366"></a><tt class="py-lineno">1366</tt>  <tt class="py-line">        <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">nanmean</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">s2</tt><tt class="py-op">)</tt> <tt class="py-op">]</tt> </tt>
<a name="L1367"></a><tt class="py-lineno">1367</tt>  <tt class="py-line">        <tt class="py-comment">#err = [sum((s-t)**2./t**2) for s, t in zip(s1, s2)]</tt> </tt>
<a name="L1368"></a><tt class="py-lineno">1368</tt>  <tt class="py-line">    <tt class="py-name">mse</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1369"></a><tt class="py-lineno">1369</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">mse</tt> </tt>
</div><a name="L1370"></a><tt class="py-lineno">1370</tt>  <tt class="py-line"> </tt>
<a name="clearNaN"></a><div id="clearNaN-def"><a name="L1371"></a><tt class="py-lineno">1371</tt> <a class="py-toggle" href="#" id="clearNaN-toggle" onclick="return toggle('clearNaN');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#clearNaN">clearNaN</a><tt class="py-op">(</tt><tt class="py-param">obs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="clearNaN-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="clearNaN-expanded"><a name="L1372"></a><tt class="py-lineno">1372</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L1373"></a><tt class="py-lineno">1373</tt>  <tt class="py-line"><tt class="py-docstring">    Loops through an array with data series as columns, and </tt> </tt>
<a name="L1374"></a><tt class="py-lineno">1374</tt>  <tt class="py-line"><tt class="py-docstring">    Replaces NaNs with the mean of the other series.</tt> </tt>
<a name="L1375"></a><tt class="py-lineno">1375</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L1376"></a><tt class="py-lineno">1376</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L1377"></a><tt class="py-lineno">1377</tt>  <tt class="py-line"><tt class="py-docstring">        - `obs`: 2-dimensional numpy array</tt> </tt>
<a name="L1378"></a><tt class="py-lineno">1378</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1379"></a><tt class="py-lineno">1379</tt>  <tt class="py-line"><tt class="py-docstring">    :Returns:</tt> </tt>
<a name="L1380"></a><tt class="py-lineno">1380</tt>  <tt class="py-line"><tt class="py-docstring">        array of the same shape as obs</tt> </tt>
<a name="L1381"></a><tt class="py-lineno">1381</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L1382"></a><tt class="py-lineno">1382</tt>  <tt class="py-line">    <tt class="py-name">rows</tt> <tt class="py-op">=</tt> <tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#tranpose to facilitate processing</tt> </tt>
<a name="L1383"></a><tt class="py-lineno">1383</tt>  <tt class="py-line">    <tt class="py-name">res</tt>  <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L1384"></a><tt class="py-lineno">1384</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt id="link-229" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-229', 'r', 'link-64');">r</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">rows</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1385"></a><tt class="py-lineno">1385</tt>  <tt class="py-line">        <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt id="link-230" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-230', 'r', 'link-64');">r</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1386"></a><tt class="py-lineno">1386</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1387"></a><tt class="py-lineno">1387</tt>  <tt class="py-line">            <tt class="py-keyword">continue</tt> </tt>
<a name="L1388"></a><tt class="py-lineno">1388</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1389"></a><tt class="py-lineno">1389</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt> <tt id="link-231" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-231', 'e', 'link-43');">e</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-232" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-232', 'r', 'link-64');">r</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1390"></a><tt class="py-lineno">1390</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt id="link-233" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-233', 'e', 'link-43');">e</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1391"></a><tt class="py-lineno">1391</tt>  <tt class="py-line">                    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1392"></a><tt class="py-lineno">1392</tt>  <tt class="py-line">                    <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">pop</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> </tt>
<a name="L1393"></a><tt class="py-lineno">1393</tt>  <tt class="py-line">                    <tt id="link-234" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-234', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">nanmean</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L1394"></a><tt class="py-lineno">1394</tt>  <tt class="py-line">                    <tt id="link-235" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-235', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt id="link-236" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-236', 'r', 'link-64');">r</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1395"></a><tt class="py-lineno">1395</tt>  <tt class="py-line">            <tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-237" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-237', 'r', 'link-64');">r</a></tt> </tt>
<a name="L1396"></a><tt class="py-lineno">1396</tt>  <tt class="py-line">                 </tt>
<a name="L1397"></a><tt class="py-lineno">1397</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">T</tt> </tt>
</div><a name="L1398"></a><tt class="py-lineno">1398</tt>  <tt class="py-line"> </tt>
<a name="enumRun"></a><div id="enumRun-def"><a name="L1399"></a><tt class="py-lineno">1399</tt> <a class="py-toggle" href="#" id="enumRun-toggle" onclick="return toggle('enumRun');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#enumRun">enumRun</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt><tt class="py-param">k</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="enumRun-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="enumRun-expanded"><a name="L1400"></a><tt class="py-lineno">1400</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L1401"></a><tt class="py-lineno">1401</tt>  <tt class="py-line"><tt class="py-docstring">    Returns model results plus run number.</tt> </tt>
<a name="L1402"></a><tt class="py-lineno">1402</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1403"></a><tt class="py-lineno">1403</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L1404"></a><tt class="py-lineno">1404</tt>  <tt class="py-line"><tt class="py-docstring">        - `model`: model callable</tt> </tt>
<a name="L1405"></a><tt class="py-lineno">1405</tt>  <tt class="py-line"><tt class="py-docstring">        - `theta`: model input list</tt> </tt>
<a name="L1406"></a><tt class="py-lineno">1406</tt>  <tt class="py-line"><tt class="py-docstring">        - `k`: run number</tt> </tt>
<a name="L1407"></a><tt class="py-lineno">1407</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1408"></a><tt class="py-lineno">1408</tt>  <tt class="py-line"><tt class="py-docstring">    :Return:</tt> </tt>
<a name="L1409"></a><tt class="py-lineno">1409</tt>  <tt class="py-line"><tt class="py-docstring">        - res: result list</tt> </tt>
<a name="L1410"></a><tt class="py-lineno">1410</tt>  <tt class="py-line"><tt class="py-docstring">        - `k`: run number</tt> </tt>
<a name="L1411"></a><tt class="py-lineno">1411</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L1412"></a><tt class="py-lineno">1412</tt>  <tt class="py-line">    <tt class="py-name">res</tt> <tt class="py-op">=</tt><tt id="link-238" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-238', 'model', 'link-22');">model</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L1413"></a><tt class="py-lineno">1413</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">,</tt><tt class="py-name">k</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1414"></a><tt class="py-lineno">1414</tt>  <tt class="py-line"> </tt>
<a name="model_as_ra"></a><div id="model_as_ra-def"><a name="L1415"></a><tt class="py-lineno">1415</tt> <a class="py-toggle" href="#" id="model_as_ra-toggle" onclick="return toggle('model_as_ra');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#model_as_ra">model_as_ra</a><tt class="py-op">(</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">phinames</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="model_as_ra-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="model_as_ra-expanded"><a name="L1416"></a><tt class="py-lineno">1416</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L1417"></a><tt class="py-lineno">1417</tt>  <tt class="py-line"><tt class="py-docstring">    Does a single run of self.model and returns the results as a record array</tt> </tt>
<a name="L1418"></a><tt class="py-lineno">1418</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L1419"></a><tt class="py-lineno">1419</tt>  <tt class="py-line">    <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L1420"></a><tt class="py-lineno">1420</tt>  <tt class="py-line">    <tt class="py-name">nphi</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">phinames</tt><tt class="py-op">)</tt> </tt>
<a name="L1421"></a><tt class="py-lineno">1421</tt>  <tt class="py-line">    <tt id="link-239" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-239', 'r', 'link-64');">r</a></tt> <tt class="py-op">=</tt> <tt id="link-240" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-240', 'model', 'link-22');">model</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L1422"></a><tt class="py-lineno">1422</tt>  <tt class="py-line">    <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt id="link-241" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-241', 'r', 'link-64');">r</a></tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">phinames</tt><tt class="py-op">)</tt> </tt>
<a name="L1423"></a><tt class="py-lineno">1423</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1424"></a><tt class="py-lineno">1424</tt>  <tt class="py-line">        <tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-242" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-242', 'r', 'link-64');">r</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L1425"></a><tt class="py-lineno">1425</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L1426"></a><tt class="py-lineno">1426</tt>  <tt class="py-line"> </tt>
<a name="model"></a><div id="model-def"><a name="L1427"></a><tt class="py-lineno">1427</tt> <a class="py-toggle" href="#" id="model-toggle" onclick="return toggle('model');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#model">model</a><tt class="py-op">(</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="model-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="model-expanded"><a name="L1428"></a><tt class="py-lineno">1428</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L1429"></a><tt class="py-lineno">1429</tt>  <tt class="py-line"><tt class="py-docstring">    Model (r,p0, n=1)</tt> </tt>
<a name="L1430"></a><tt class="py-lineno">1430</tt>  <tt class="py-line"><tt class="py-docstring">    Simulates the Population dynamic Model (PDM) Pt = rP0</tt> </tt>
<a name="L1431"></a><tt class="py-lineno">1431</tt>  <tt class="py-line"><tt class="py-docstring">    for n time steps.</tt> </tt>
<a name="L1432"></a><tt class="py-lineno">1432</tt>  <tt class="py-line"><tt class="py-docstring">    P0 is the initial population size. </tt> </tt>
<a name="L1433"></a><tt class="py-lineno">1433</tt>  <tt class="py-line"><tt class="py-docstring">    Example model for testing purposes.</tt> </tt>
<a name="L1434"></a><tt class="py-lineno">1434</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L1435"></a><tt class="py-lineno">1435</tt>  <tt class="py-line">    <tt id="link-243" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-243', 'r', 'link-64');">r</a></tt><tt class="py-op">,</tt> <tt class="py-name">p0</tt> <tt class="py-op">=</tt> <tt class="py-name">theta</tt> </tt>
<a name="L1436"></a><tt class="py-lineno">1436</tt>  <tt class="py-line"><tt class="py-comment">#    print "oi"</tt> </tt>
<a name="L1437"></a><tt class="py-lineno">1437</tt>  <tt class="py-line">    <tt class="py-name">Pt</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt> <tt class="py-comment"># initialize the output vector</tt> </tt>
<a name="L1438"></a><tt class="py-lineno">1438</tt>  <tt class="py-line">    <tt class="py-name">P</tt> <tt class="py-op">=</tt> <tt class="py-name">p0</tt> </tt>
<a name="L1439"></a><tt class="py-lineno">1439</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1440"></a><tt class="py-lineno">1440</tt>  <tt class="py-line">        <tt class="py-name">Pt</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-244" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-244', 'r', 'link-64');">r</a></tt><tt class="py-op">*</tt><tt class="py-name">P</tt> </tt>
<a name="L1441"></a><tt class="py-lineno">1441</tt>  <tt class="py-line">        <tt class="py-name">P</tt> <tt class="py-op">=</tt> <tt class="py-name">Pt</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L1442"></a><tt class="py-lineno">1442</tt>  <tt class="py-line">     </tt>
<a name="L1443"></a><tt class="py-lineno">1443</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">Pt</tt> </tt>
</div><a name="L1444"></a><tt class="py-lineno">1444</tt>  <tt class="py-line"> </tt>
<a name="L1445"></a><tt class="py-lineno">1445</tt>  <tt class="py-line"> </tt>
<a name="plotRaHist"></a><div id="plotRaHist-def"><a name="L1446"></a><tt class="py-lineno">1446</tt> <a class="py-toggle" href="#" id="plotRaHist-toggle" onclick="return toggle('plotRaHist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#plotRaHist">plotRaHist</a><tt class="py-op">(</tt><tt class="py-param">arr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plotRaHist-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="plotRaHist-expanded"><a name="L1447"></a><tt class="py-lineno">1447</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L1448"></a><tt class="py-lineno">1448</tt>  <tt class="py-line"><tt class="py-docstring">    Plots a record array</tt> </tt>
<a name="L1449"></a><tt class="py-lineno">1449</tt>  <tt class="py-line"><tt class="py-docstring">    as a panel of histograms</tt> </tt>
<a name="L1450"></a><tt class="py-lineno">1450</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L1451"></a><tt class="py-lineno">1451</tt>  <tt class="py-line">    <tt class="py-name">nv</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">arr</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L1452"></a><tt class="py-lineno">1452</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ceil</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-comment">#figure size</tt> </tt>
<a name="L1453"></a><tt class="py-lineno">1453</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1454"></a><tt class="py-lineno">1454</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">arr</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1455"></a><tt class="py-lineno">1455</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1456"></a><tt class="py-lineno">1456</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">hist</tt><tt class="py-op">(</tt><tt class="py-name">arr</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">bins</tt><tt class="py-op">=</tt><tt class="py-number">50</tt><tt class="py-op">,</tt> <tt class="py-name">normed</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L1457"></a><tt class="py-lineno">1457</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1458"></a><tt class="py-lineno">1458</tt>  <tt class="py-line"> </tt>
<a name="L1459"></a><tt class="py-lineno">1459</tt>  <tt class="py-line"> </tt>
<a name="main2"></a><div id="main2-def"><a name="L1460"></a><tt class="py-lineno">1460</tt> <a class="py-toggle" href="#" id="main2-toggle" onclick="return toggle('main2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#main2">main2</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main2-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="main2-expanded"><a name="L1461"></a><tt class="py-lineno">1461</tt>  <tt class="py-line">    <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1462"></a><tt class="py-lineno">1462</tt>  <tt class="py-line">    <tt class="py-comment">#Me = Meld(K=5000,L=1000,model=model, ntheta=2,nphi=1,verbose=False,viz=False)</tt> </tt>
<a name="L1463"></a><tt class="py-lineno">1463</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.setTheta" class="py-name" href="#" onclick="return doclink('link-245', 'setTheta', 'link-48');">setTheta</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'p0'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1464"></a><tt class="py-lineno">1464</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.setPhi" class="py-name" href="#" onclick="return doclink('link-246', 'setPhi', 'link-49');">setPhi</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'p'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1465"></a><tt class="py-lineno">1465</tt>  <tt class="py-line">    <tt class="py-comment">#Me.add_data(normal(7.5,1,400),'normal',(6,9))</tt> </tt>
<a name="L1466"></a><tt class="py-lineno">1466</tt>  <tt class="py-line">    <tt class="py-comment">#Me.run()</tt> </tt>
<a name="L1467"></a><tt class="py-lineno">1467</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.sir" class="py-name" href="#" onclick="return doclink('link-247', 'sir', 'link-51');">sir</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'p'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-number">7.5</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> <tt class="py-op">)</tt> </tt>
<a name="L1468"></a><tt class="py-lineno">1468</tt>  <tt class="py-line">    <tt id="link-248" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-248', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt> <tt class="py-op">=</tt> <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-249', 'getPosteriors', 'link-53');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1469"></a><tt class="py-lineno">1469</tt>  <tt class="py-line">    <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1470"></a><tt class="py-lineno">1470</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">end</tt><tt class="py-op">-</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-string">' seconds'</tt> </tt>
<a name="L1471"></a><tt class="py-lineno">1471</tt>  <tt class="py-line">    <tt id="link-250" class="py-name" targets="Function trunk.BIP.Bayes.Melding.plotRaHist()=trunk.BIP.Bayes.Melding-module.html#plotRaHist"><a title="trunk.BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-250', 'plotRaHist', 'link-250');">plotRaHist</a></tt><tt class="py-op">(</tt><tt id="link-251" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-251', 'pt', 'link-52');">pt</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1472"></a><tt class="py-lineno">1472</tt>  <tt class="py-line">    <tt id="link-252" class="py-name"><a title="trunk.BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-252', 'plotRaHist', 'link-250');">plotRaHist</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt> </tt>
<a name="L1473"></a><tt class="py-lineno">1473</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1474"></a><tt class="py-lineno">1474</tt>  <tt class="py-line">     </tt>
<a name="L1475"></a><tt class="py-lineno">1475</tt>  <tt class="py-line">     </tt>
<a name="mh_test"></a><div id="mh_test-def"><a name="L1476"></a><tt class="py-lineno">1476</tt> <a class="py-toggle" href="#" id="mh_test-toggle" onclick="return toggle('mh_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Melding-module.html#mh_test">mh_test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="mh_test-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="mh_test-expanded"><a name="L1477"></a><tt class="py-lineno">1477</tt>  <tt class="py-line">    <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1478"></a><tt class="py-lineno">1478</tt>  <tt class="py-line">    <tt class="py-comment">#Me = Meld(K=5000,L=1000,model=model, ntheta=2,nphi=1,verbose=False,viz=False)</tt> </tt>
<a name="L1479"></a><tt class="py-lineno">1479</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.setTheta" class="py-name" href="#" onclick="return doclink('link-253', 'setTheta', 'link-48');">setTheta</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'p0'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1480"></a><tt class="py-lineno">1480</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-254" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.setPhi" class="py-name" href="#" onclick="return doclink('link-254', 'setPhi', 'link-49');">setPhi</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'p'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1481"></a><tt class="py-lineno">1481</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.mcmc_run" class="py-name" href="#" onclick="return doclink('link-255', 'mcmc_run', 'link-54');">mcmc_run</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'p'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-number">7.5</tt><tt class="py-op">]</tt><tt class="py-op">}</tt><tt class="py-op">,</tt><tt class="py-name">burnin</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt> </tt>
<a name="L1482"></a><tt class="py-lineno">1482</tt>  <tt class="py-line">    <tt id="link-256" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-256', 'pt', 'link-52');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt> <tt class="py-op">=</tt> <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-257', 'getPosteriors', 'link-53');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1483"></a><tt class="py-lineno">1483</tt>  <tt class="py-line">    <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1484"></a><tt class="py-lineno">1484</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">end</tt><tt class="py-op">-</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-string">' seconds'</tt> </tt>
<a name="L1485"></a><tt class="py-lineno">1485</tt>  <tt class="py-line">    <tt id="link-258" class="py-name"><a title="trunk.BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-258', 'plotRaHist', 'link-250');">plotRaHist</a></tt><tt class="py-op">(</tt><tt id="link-259" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-259', 'pt', 'link-52');">pt</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1486"></a><tt class="py-lineno">1486</tt>  <tt class="py-line">    <tt id="link-260" class="py-name"><a title="trunk.BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-260', 'plotRaHist', 'link-250');">plotRaHist</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt> </tt>
<a name="L1487"></a><tt class="py-lineno">1487</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1488"></a><tt class="py-lineno">1488</tt>  <tt class="py-line">     </tt>
<a name="L1489"></a><tt class="py-lineno">1489</tt>  <tt class="py-line"> </tt>
<a name="L1490"></a><tt class="py-lineno">1490</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L1491"></a><tt class="py-lineno">1491</tt>  <tt class="py-line">    <tt class="py-name">Me</tt> <tt class="py-op">=</tt> <tt id="link-261" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld" class="py-name" href="#" onclick="return doclink('link-261', 'Meld', 'link-27');">Meld</a></tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">=</tt><tt class="py-number">5000</tt><tt class="py-op">,</tt><tt class="py-name">L</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">,</tt><tt id="link-262" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-262', 'model', 'link-22');">model</a></tt><tt class="py-op">=</tt><tt id="link-263" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-263', 'model', 'link-22');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">ntheta</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nphi</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">verbose</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt><tt id="link-264" class="py-name"><a title="trunk.BIP.SDE.gillespie.viz" class="py-name" href="#" onclick="return doclink('link-264', 'viz', 'link-122');">viz</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L1492"></a><tt class="py-lineno">1492</tt>  <tt class="py-line">    <tt class="py-comment">#mh_test()</tt> </tt>
<a name="L1493"></a><tt class="py-lineno">1493</tt>  <tt class="py-line">    <tt id="link-265" class="py-name" targets="Function trunk.BIP.Bayes.Melding.main2()=trunk.BIP.Bayes.Melding-module.html#main2"><a title="trunk.BIP.Bayes.Melding.main2" class="py-name" href="#" onclick="return doclink('link-265', 'main2', 'link-265');">main2</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1494"></a><tt class="py-lineno">1494</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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